From k at dev.open-bio.org  Fri Feb  1 22:36:00 2008
From: k at dev.open-bio.org (Katayama Toshiaki)
Date: Sat, 02 Feb 2008 03:36:00 +0000
Subject: [BioRuby-cvs] bioruby ChangeLog,1.80,1.81
Message-ID: <200802020336.m123a0gr029664@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby
In directory dev.open-bio.org:/tmp/cvs-serv29660

Modified Files:
	ChangeLog 
Log Message:
* lib/bio/shell/rails/vendor/plugins/

The 'generators' directory is moved under the 'bioruby' subdirectory
so that 'bioruby --rails' command can work with Rails 2.x series
in addition to the Rails 1.2.x series.



Index: ChangeLog
===================================================================
RCS file: /home/repository/bioruby/bioruby/ChangeLog,v
retrieving revision 1.80
retrieving revision 1.81
diff -C2 -d -r1.80 -r1.81
*** ChangeLog	9 Jan 2008 17:22:39 -0000	1.80
--- ChangeLog	2 Feb 2008 03:35:58 -0000	1.81
***************
*** 1,4 ****
--- 1,12 ----
  2008-01-10  Toshiaki Katayama <k at bioruby.org>
  
+ 	* lib/bio/shell/rails/vendor/plugins/
+ 
+ 	  The 'generators' directory is moved under the 'bioruby' subdirectory
+ 	  so that 'bioruby --rails' command can work with Rails 2.x series
+ 	  in addition to the Rails 1.2.x series.
+ 
+ 2008-01-10  Toshiaki Katayama <k at bioruby.org>
+ 
  	* lib/bio/io/hinv.rb
  


From k at dev.open-bio.org  Fri Feb  1 22:54:50 2008
From: k at dev.open-bio.org (Katayama Toshiaki)
Date: Sat, 02 Feb 2008 03:54:50 +0000
Subject: [BioRuby-cvs] bioruby ChangeLog,1.81,1.82
Message-ID: <200802020354.m123soGS029686@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby
In directory dev.open-bio.org:/tmp/cvs-serv29682

Modified Files:
	ChangeLog 
Log Message:
fix typo


Index: ChangeLog
===================================================================
RCS file: /home/repository/bioruby/bioruby/ChangeLog,v
retrieving revision 1.81
retrieving revision 1.82
diff -C2 -d -r1.81 -r1.82
*** ChangeLog	2 Feb 2008 03:35:58 -0000	1.81
--- ChangeLog	2 Feb 2008 03:54:48 -0000	1.82
***************
*** 1,3 ****
! 2008-01-10  Toshiaki Katayama <k at bioruby.org>
  
  	* lib/bio/shell/rails/vendor/plugins/
--- 1,3 ----
! 2008-02-02  Toshiaki Katayama <k at bioruby.org>
  
  	* lib/bio/shell/rails/vendor/plugins/


From ngoto at dev.open-bio.org  Mon Feb 11 21:13:34 2008
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Tue, 12 Feb 2008 02:13:34 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/blast format0.rb,1.25,1.26
Message-ID: <200802120213.m1C2DX5m009903@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/blast
In directory dev.open-bio.org:/tmp/cvs-serv9861/lib/bio/appl/blast

Modified Files:
	format0.rb 
Log Message:
* Bug fixes reported by Shuji Shigenobu.
  * Failed to parse query length for long query (>= 10000 letters)
    because comma is inserted for digit separator by blastall.
  * Failed to parse e-value for some BLASTX results


Index: format0.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast/format0.rb,v
retrieving revision 1.25
retrieving revision 1.26
diff -C2 -d -r1.25 -r1.26
*** format0.rb	27 Dec 2007 17:28:57 -0000	1.25
--- format0.rb	12 Feb 2008 02:13:31 -0000	1.26
***************
*** 265,270 ****
                  q << sc.scan(/.*/)
                  sc.skip(/\s*^ ?/)
!               end until !sc.rest or r = sc.skip(/ *\( *(\d+) *letters *\)\s*\z/)
!               @query_len = sc[1].to_i if r
                @query_def = q.join(' ')
              end
--- 265,270 ----
                  q << sc.scan(/.*/)
                  sc.skip(/\s*^ ?/)
!               end until !sc.rest or r = sc.skip(/ *\( *([\,\d]+) *letters *\)\s*\z/)
!               @query_len = sc[1].delete(',').to_i if r
                @query_def = q.join(' ')
              end
***************
*** 969,973 ****
                while sc.rest?
                  sc.skip(/\s*/)
!                 if sc.skip(/Expect(?:\(\d\))? *\= *([e\-\.\d]+)/) then
                    ev = sc[1].to_s
                    ev = '1' + ev if ev[0] == ?e
--- 969,973 ----
                while sc.rest?
                  sc.skip(/\s*/)
!                 if sc.skip(/Expect(?:\(\d+\))? *\= *([e\-\.\d]+)/) then
                    ev = sc[1].to_s
                    ev = '1' + ev if ev[0] == ?e


From ngoto at dev.open-bio.org  Tue Feb 12 00:32:25 2008
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Tue, 12 Feb 2008 05:32:25 +0000
Subject: [BioRuby-cvs] bioruby ChangeLog,1.82,1.83
Message-ID: <200802120532.m1C5WP5M011183@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby
In directory dev.open-bio.org:/tmp/cvs-serv11163

Modified Files:
	ChangeLog 
Log Message:
ChangeLog for lib/bio/appl/blast/format0.rb from 1.25 to 1.26.


Index: ChangeLog
===================================================================
RCS file: /home/repository/bioruby/bioruby/ChangeLog,v
retrieving revision 1.82
retrieving revision 1.83
diff -C2 -d -r1.82 -r1.83
*** ChangeLog	2 Feb 2008 03:54:48 -0000	1.82
--- ChangeLog	12 Feb 2008 05:32:23 -0000	1.83
***************
*** 1,2 ****
--- 1,11 ----
+ 2008-02-12  Naohisa Goto <ng at bioruby.org>
+ 
+ 	* lib/bio/appl/blast/format0.rb
+ 
+ 	  Fixed bugs: Failed to parse query length for long query
+ 	  (>= 10000 letters) as comma is inserted for digit separator
+ 	  by blastall; Failed to parse e-value for some BLASTX results.
+ 	  Thanks to Shuji Shigenobu who reported the bugs and sent patches.
+ 
  2008-02-02  Toshiaki Katayama <k at bioruby.org>
  


From ngoto at dev.open-bio.org  Wed Feb 13 05:28:20 2008
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Wed, 13 Feb 2008 10:28:20 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio sequence.rb,0.58,0.58.2.1
Message-ID: <200802131028.m1DASKHe017196@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv17175/lib/bio

Modified Files:
      Tag: BRANCH-biohackathon2008
	sequence.rb 
Log Message:
Added a new class method Bio::Sequence.read(str).


Index: sequence.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence.rb,v
retrieving revision 0.58
retrieving revision 0.58.2.1
diff -C2 -d -r0.58 -r0.58.2.1
*** sequence.rb	5 Apr 2007 23:35:39 -0000	0.58
--- sequence.rb	13 Feb 2008 10:28:16 -0000	0.58.2.1
***************
*** 334,337 ****
--- 334,356 ----
      @moltype = AA
    end
+ 
+   # Create a new Bio::Sequence object from a formatted string
+   # (GenBank, EMBL, fasta format, etc.)
+   #
+   #   s = Bio::Sequence.read(str)
+   # ---
+   # *Arguments*:
+   # * (required) _str_: string
+   # * (optional) _format_: format specification (class or nil)
+   # *Returns*:: Bio::Sequence object
+   def self.read(str, format = nil)
+     if format then
+       klass = format
+     else
+       klass = Bio::FlatFile::AutoDetect.default.guess(str)
+     end
+     obj = klass.new(str)
+     obj.to_biosequence
+   end
    
  end # Sequence


From ngoto at dev.open-bio.org  Wed Feb 13 22:13:48 2008
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Thu, 14 Feb 2008 03:13:48 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/sequence format.rb,1.4,1.4.2.1
Message-ID: <200802140313.m1E3Dm2s019722@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/sequence
In directory dev.open-bio.org:/tmp/cvs-serv19681/lib/bio/sequence

Modified Files:
      Tag: BRANCH-biohackathon2008
	format.rb 
Log Message:
* lib/bio/sequence.rb
  * changed to include Format module
* lib/bio/sequence/format.rb
  * fixed bug: incorrect refactoring


Index: format.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence/format.rb,v
retrieving revision 1.4
retrieving revision 1.4.2.1
diff -C2 -d -r1.4 -r1.4.2.1
*** format.rb	5 Apr 2007 23:35:41 -0000	1.4
--- format.rb	14 Feb 2008 03:13:46 -0000	1.4.2.1
***************
*** 18,23 ****
  module Bio
  
-   autoload :Sequence, 'bio/sequence'
- 
  class Sequence
  
--- 18,21 ----
***************
*** 127,131 ****
  
    def format_qualifiers(qualifiers, indent, width)
!     qualifiers.each do |qualifier|
        q = qualifier.qualifier
        v = qualifier.value.to_s
--- 125,129 ----
  
    def format_qualifiers(qualifiers, indent, width)
!     qualifiers.collect do |qualifier|
        q = qualifier.qualifier
        v = qualifier.value.to_s
***************
*** 134,138 ****
          lines = wrap('/' + q, width)
        elsif q == 'translation'
!         lines = fold('/' + q + '=' + val, width)
        else
          if v[/\D/]
--- 132,136 ----
          lines = wrap('/' + q, width)
        elsif q == 'translation'
!         lines = fold('/' + q + '=' + v, width)
        else
          if v[/\D/]
***************
*** 141,149 ****
            v = '"' + v + '"'
          end
!         lines = wrap('/' + q + '=' + val, width)
        end
  
!       return lines.gsub(/^/, indent)
!     end
    end
  
--- 139,148 ----
            v = '"' + v + '"'
          end
!         lines = wrap('/' + q + '=' + v, width)
        end
  
!       lines.gsub!(/^/, indent)
!       lines
!     end.join
    end
  


From ngoto at dev.open-bio.org  Wed Feb 13 22:13:48 2008
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Thu, 14 Feb 2008 03:13:48 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio sequence.rb,0.58.2.1,0.58.2.2
Message-ID: <200802140313.m1E3DmsN019717@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv19681/lib/bio

Modified Files:
      Tag: BRANCH-biohackathon2008
	sequence.rb 
Log Message:
* lib/bio/sequence.rb
  * changed to include Format module
* lib/bio/sequence/format.rb
  * fixed bug: incorrect refactoring


Index: sequence.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence.rb,v
retrieving revision 0.58.2.1
retrieving revision 0.58.2.2
diff -C2 -d -r0.58.2.1 -r0.58.2.2
*** sequence.rb	13 Feb 2008 10:28:16 -0000	0.58.2.1
--- sequence.rb	14 Feb 2008 03:13:46 -0000	0.58.2.2
***************
*** 71,74 ****
--- 71,75 ----
    autoload :Generic, 'bio/sequence/generic'
    autoload :Format,  'bio/sequence/format'
+   include Format
  
    # Create a new Bio::Sequence object
***************
*** 149,153 ****
    # *Returns*:: String object
    def output(style)
-     extend Bio::Sequence::Format
      case style
      when :fasta
--- 150,153 ----


From ngoto at dev.open-bio.org  Wed Feb 13 22:32:16 2008
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Thu, 14 Feb 2008 03:32:16 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/sequence format.rb,1.4.2.1,1.4.2.2
Message-ID: <200802140332.m1E3WGAu019905@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/sequence
In directory dev.open-bio.org:/tmp/cvs-serv19885/lib/bio/sequence

Modified Files:
      Tag: BRANCH-biohackathon2008
	format.rb 
Log Message:
in wrap(), the last "\n" should be added for non-empty string


Index: format.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence/format.rb,v
retrieving revision 1.4.2.1
retrieving revision 1.4.2.2
diff -C2 -d -r1.4.2.1 -r1.4.2.2
*** format.rb	14 Feb 2008 03:13:46 -0000	1.4.2.1
--- format.rb	14 Feb 2008 03:32:14 -0000	1.4.2.2
***************
*** 170,174 ****
      end
      result << left if left
!     return result.join("\n")
    end
  
--- 170,176 ----
      end
      result << left if left
!     result_string = result.join("\n")
!     result_string << "\n" unless result_string.empty?
!     return result_string
    end
  


From ngoto at dev.open-bio.org  Thu Feb 14 03:51:47 2008
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Thu, 14 Feb 2008 08:51:47 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/db/genbank genbank.rb,0.40,0.40.2.1
Message-ID: <200802140851.m1E8plsw023607@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/db/genbank
In directory dev.open-bio.org:/tmp/cvs-serv23587/lib/bio/db/genbank

Modified Files:
      Tag: BRANCH-biohackathon2008
	genbank.rb 
Log Message:
added new method Bio::GenBank#to_biosequence.


Index: genbank.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/genbank/genbank.rb,v
retrieving revision 0.40
retrieving revision 0.40.2.1
diff -C2 -d -r0.40 -r0.40.2.1
*** genbank.rb	5 Apr 2007 23:35:40 -0000	0.40
--- genbank.rb	14 Feb 2008 08:51:45 -0000	0.40.2.1
***************
*** 126,129 ****
--- 126,157 ----
    end
  
+   # converts Bio::GenBank to Bio::Sequence
+   # ---
+   # *Arguments*: 
+   # *Returns*:: Bio::Sequence object
+   def to_biosequence
+     sequence = Bio::Sequence.new(seq)
+     sequence.entry_id = self.entry_id
+ 
+     sequence.primary_accession = self.accession
+     sequence.secondary_accessions = self.accessions - [ self.accession ]
+ 
+     sequence.molecule_type = self.natype
+     sequence.division = self.division
+     sequence.topology = self.circular
+ 
+     sequence.sequence_version = self.version
+     seq.date_created = nil #????
+     sequence.date_modified = self.date
+ 
+     sequence.keywords = self.keywords
+     sequence.species = self.organism
+     sequence.classification = self.taxonomy
+     sequence.organnella = nil # not used
+     sequence.comments = self.comment
+     sequence.references = self.references
+     return sequence
+   end
+ 
  end # GenBank
  end # Bio


From ngoto at dev.open-bio.org  Thu Feb 14 21:18:24 2008
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Fri, 15 Feb 2008 02:18:24 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/sequence format.rb,1.4.2.2,1.4.2.3
Message-ID: <200802150218.m1F2IOnH025723@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/sequence
In directory dev.open-bio.org:/tmp/cvs-serv25703/lib/bio/sequence

Modified Files:
      Tag: BRANCH-biohackathon2008
	format.rb 
Log Message:
special character in regexp should be escaped


Index: format.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence/format.rb,v
retrieving revision 1.4.2.2
retrieving revision 1.4.2.3
diff -C2 -d -r1.4.2.2 -r1.4.2.3
*** format.rb	14 Feb 2008 03:32:14 -0000	1.4.2.2
--- format.rb	15 Feb 2008 02:18:21 -0000	1.4.2.3
***************
*** 157,161 ****
        line = nil
        width.downto(1) do |i|
!         if left[i..i] == ' ' or /[,;]/ =~ left[(i-1)..(i-1)]  then
            line = left[0..(i-1)].sub(/ +\z/, '')
            left = left[i..-1].sub(/\A +/, '')
--- 157,161 ----
        line = nil
        width.downto(1) do |i|
!         if left[i..i] == ' ' or /[\,\;]/ =~ left[(i-1)..(i-1)]  then
            line = left[0..(i-1)].sub(/ +\z/, '')
            left = left[i..-1].sub(/\A +/, '')


From ngoto at dev.open-bio.org  Thu Feb 14 22:23:25 2008
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Fri, 15 Feb 2008 03:23:25 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio sequence.rb,0.58.2.2,0.58.2.3
Message-ID: <200802150323.m1F3NP8b025922@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv25902/lib/bio

Modified Files:
      Tag: BRANCH-biohackathon2008
	sequence.rb 
Log Message:
In Bio::Sequence#method_missing, __send__ should be used instead of 
send. When method is not found, error message is modified if it is 
caused by method_missing.


Index: sequence.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence.rb,v
retrieving revision 0.58.2.2
retrieving revision 0.58.2.3
diff -C2 -d -r0.58.2.2 -r0.58.2.3
*** sequence.rb	14 Feb 2008 03:13:46 -0000	0.58.2.2
--- sequence.rb	15 Feb 2008 03:23:23 -0000	0.58.2.3
***************
*** 97,101 ****
    # http://www.rubycentral.com/book/ref_c_object.html#Object.method_missing
    def method_missing(sym, *args, &block) #:nodoc:
!     @seq.send(sym, *args, &block)
    end
    
--- 97,119 ----
    # http://www.rubycentral.com/book/ref_c_object.html#Object.method_missing
    def method_missing(sym, *args, &block) #:nodoc:
!     begin
!       @seq.__send__(sym, *args, &block)
!     rescue NoMethodError => evar
!       lineno = __LINE__ - 2
!       file = __FILE__
!       bt_here = [ "#{file}:#{lineno}:in \`__send__\'",
!                   "#{file}:#{lineno}:in \`method_missing\'"
!                 ]
!       if bt_here == evar.backtrace[0, 2] then
!         bt = evar.backtrace[2..-1]
!         evar = NoMethodError.new("undefined method \`#{sym.to_s}\' for #{self.inspect}")
!         evar.set_backtrace(bt)
!       end
!       #p lineno
!       #p file
!       #p bt_here
!       #p evar.backtrace
!       raise(evar)
!     end
    end
    


From ngoto at dev.open-bio.org  Thu Feb 14 22:33:53 2008
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Fri, 15 Feb 2008 03:33:53 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio sequence.rb,0.58.2.3,0.58.2.4
Message-ID: <200802150333.m1F3Xr5w025971@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv25951/lib/bio

Modified Files:
      Tag: BRANCH-biohackathon2008
	sequence.rb 
Log Message:
changed to use original exception class instead of NoMethodError 


Index: sequence.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence.rb,v
retrieving revision 0.58.2.3
retrieving revision 0.58.2.4
diff -C2 -d -r0.58.2.3 -r0.58.2.4
*** sequence.rb	15 Feb 2008 03:23:23 -0000	0.58.2.3
--- sequence.rb	15 Feb 2008 03:33:51 -0000	0.58.2.4
***************
*** 107,111 ****
        if bt_here == evar.backtrace[0, 2] then
          bt = evar.backtrace[2..-1]
!         evar = NoMethodError.new("undefined method \`#{sym.to_s}\' for #{self.inspect}")
          evar.set_backtrace(bt)
        end
--- 107,111 ----
        if bt_here == evar.backtrace[0, 2] then
          bt = evar.backtrace[2..-1]
!         evar = evar.class.new("undefined method \`#{sym.to_s}\' for #{self.inspect}")
          evar.set_backtrace(bt)
        end


From aerts at dev.open-bio.org  Thu Feb 14 23:49:39 2008
From: aerts at dev.open-bio.org (Jan Aerts)
Date: Fri, 15 Feb 2008 04:49:39 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/db/embl embl.rb,1.29,1.29.2.1
Message-ID: <200802150449.m1F4ndLY026633@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/db/embl
In directory dev.open-bio.org:/tmp/cvs-serv26608/db/embl

Modified Files:
      Tag: BRANCH-biohackathon2008
	embl.rb 
Log Message:
Added functionality to convert a Bio::EMBL object into a full-blown Bio::Sequence object that contains features, references and other additional 
information.


Index: embl.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/embl.rb,v
retrieving revision 1.29
retrieving revision 1.29.2.1
diff -C2 -d -r1.29 -r1.29.2.1
*** embl.rb	5 Apr 2007 23:35:40 -0000	1.29
--- embl.rb	15 Feb 2008 04:49:37 -0000	1.29.2.1
***************
*** 3,7 ****
  #
  # 
! # Copyright::   Copyright (C) 2001-2007 Mitsuteru C. Nakao <n at bioruby.org>
  # License::     The Ruby License
  #
--- 3,9 ----
  #
  # 
! # Copyright::   Copyright (C) 2001-2007
! #               Mitsuteru C. Nakao <n at bioruby.org>
! #               Jan Aerts <jan.aerts at bbsrc.ac.uk>
  # License::     The Ruby License
  #
***************
*** 121,124 ****
--- 123,130 ----
    alias molecule_type molecule
  
+   def topology
+     id_line('TOPOLOGY')
+   end
+   
    # returns DIVISION in the ID line.
    # * Bio::EMBL#division -> String
***************
*** 222,227 ****
    #
    # Bio::EMBLDB#ref
! 
! 
    ##
    # DR Line; defabases cross-regerence (>=0)
--- 228,233 ----
    #
    # Bio::EMBLDB#ref
!   
!   
    ##
    # DR Line; defabases cross-regerence (>=0)
***************
*** 356,366 ****
    # bb Line; (blanks) sequence data (>=1)
    def seq
!     Sequence::NA.new( fetch('').gsub(/ /,'').gsub(/\d+/,'') )
    end
    alias naseq seq
    alias ntseq seq
! 
    # // Line; termination line (end; 1/entry)
  
  
    ### private methods
--- 362,392 ----
    # bb Line; (blanks) sequence data (>=1)
    def seq
!     Bio::Sequence::NA.new( fetch('').gsub(/ /,'').gsub(/\d+/,'') )
    end
    alias naseq seq
    alias ntseq seq
!   
    # // Line; termination line (end; 1/entry)
  
+   def to_biosequence
+     bio_seq = Bio::Sequence.new(self.seq)
+     bio_seq.entry_id = self.entry_id
+     bio_seq.primary_accession = self.accessions[0]
+     bio_seq.secondary_accessions = self.accessions[1,-1]
+     bio_seq.molecule_type = self.molecule_type
+     bio_seq.definition = self.description
+     bio_seq.topology = self.topology
+     bio_seq.date_created = self.dt['created']
+     bio_seq.date_modified = self.dt['updated']
+     bio_seq.division = self.division
+     bio_seq.sequence_version = self.version
+     bio_seq.keywords = self.keywords
+     bio_seq.species = self.os(0)[0]['os'] + ' ' + self.os(0)[0]['name']
+     bio_seq.classification = self.oc
+     bio_seq.references = self.references
+     bio_seq.features = self.ft
+     
+     return bio_seq
+   end
  
    ### private methods
***************
*** 401,402 ****
--- 427,443 ----
  
  end # module Bio
+ 
+ if __FILE__ == $0
+   require '../../../bio'
+   require 'yaml'
+   
+   prefix = 'FT   '
+   indent = prefix + ' ' * 16
+   fwidth = 80 - indent.length
+   
+   parser = Bio::FlatFile.auto('/home/aertsj/LocalDocuments/hackathon/aj224122.embl')
+   parser.each do |entry|
+ #    entry.ref
+     puts entry.to_biosequence.output(:embl)
+   end
+ end
\ No newline at end of file


From aerts at dev.open-bio.org  Thu Feb 14 23:49:39 2008
From: aerts at dev.open-bio.org (Jan Aerts)
Date: Fri, 15 Feb 2008 04:49:39 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio sequence.rb,0.58.2.4,0.58.2.5
Message-ID: <200802150449.m1F4ndul026630@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv26608

Modified Files:
      Tag: BRANCH-biohackathon2008
	sequence.rb 
Log Message:
Added functionality to convert a Bio::EMBL object into a full-blown Bio::Sequence object that contains features, references and other additional 
information.


Index: sequence.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence.rb,v
retrieving revision 0.58.2.4
retrieving revision 0.58.2.5
diff -C2 -d -r0.58.2.4 -r0.58.2.5
*** sequence.rb	15 Feb 2008 03:33:51 -0000	0.58.2.4
--- sequence.rb	15 Feb 2008 04:49:37 -0000	0.58.2.5
***************
*** 13,16 ****
--- 13,17 ----
  #
  
+ require 'erb'
  require 'bio/sequence/compat'
  
***************
*** 73,76 ****
--- 74,79 ----
    include Format
  
+   attr_accessor :sequence_version, :topology, :molecule_type, :data_class, :division, :primary_accession, :secondary_accessions, :date_created, :date_modified, :species, :classification
+ 
    # Create a new Bio::Sequence object
    #
***************
*** 165,181 ****
    # ---
    # *Arguments*: 
!   # * (required) _style_: :fasta, :genbank, *or* :embl
    # *Returns*:: String object
!   def output(style)
!     case style
!     when :fasta
!       format_fasta
!     when :gff
!       format_gff
!     when :genbank
!       format_genbank
!     when :embl
!       format_embl
!     end
    end
  
--- 168,176 ----
    # ---
    # *Arguments*: 
!   # * (required) _format_: :fasta, :genbank, *or* :embl
    # *Returns*:: String object
!   def output(format = :fasta)
!     record_template = ERB.new(File.read(File.dirname(__FILE__) + "/db/#{format.to_s}/format.erb"))
!     record_template.result(binding)
    end
  
***************
*** 372,375 ****
--- 367,375 ----
    end
    
+   
+   def accessions
+     return [@primary_accession, @secondary_accessions].flatten
+   end
+   
  end # Sequence
  
***************
*** 380,510 ****
  if __FILE__ == $0
  
!   puts "== Test Bio::Sequence::NA.new"
!   p Bio::Sequence::NA.new('')
!   p na = Bio::Sequence::NA.new('atgcatgcATGCATGCAAAA')
!   p rna = Bio::Sequence::NA.new('augcaugcaugcaugcaaaa')
! 
!   puts "\n== Test Bio::Sequence::AA.new"
!   p Bio::Sequence::AA.new('')
!   p aa = Bio::Sequence::AA.new('ACDEFGHIKLMNPQRSTVWYU')
! 
!   puts "\n== Test Bio::Sequence#to_s"
!   p na.to_s
!   p aa.to_s
! 
!   puts "\n== Test Bio::Sequence#subseq(2,6)"
!   p na
!   p na.subseq(2,6)
! 
!   puts "\n== Test Bio::Sequence#[2,6]"
!   p na
!   p na[2,6]
! 
!   puts "\n== Test Bio::Sequence#to_fasta('hoge', 8)"
!   puts na.to_fasta('hoge', 8)
! 
!   puts "\n== Test Bio::Sequence#window_search(15)"
!   p na
!   na.window_search(15) {|x| p x}
! 
!   puts "\n== Test Bio::Sequence#total({'a'=>0.1,'t'=>0.2,'g'=>0.3,'c'=>0.4})"
!   p na.total({'a'=>0.1,'t'=>0.2,'g'=>0.3,'c'=>0.4})
! 
!   puts "\n== Test Bio::Sequence#composition"
!   p na
!   p na.composition
!   p rna
!   p rna.composition
! 
!   puts "\n== Test Bio::Sequence::NA#splicing('complement(join(1..5,16..20))')"
!   p na
!   p na.splicing("complement(join(1..5,16..20))")
!   p rna
!   p rna.splicing("complement(join(1..5,16..20))")
! 
!   puts "\n== Test Bio::Sequence::NA#complement"
!   p na.complement
!   p rna.complement
!   p Bio::Sequence::NA.new('tacgyrkmhdbvswn').complement
!   p Bio::Sequence::NA.new('uacgyrkmhdbvswn').complement
! 
!   puts "\n== Test Bio::Sequence::NA#translate"
!   p na
!   p na.translate
!   p rna
!   p rna.translate
! 
!   puts "\n== Test Bio::Sequence::NA#gc_percent"
!   p na.gc_percent
!   p rna.gc_percent
! 
!   puts "\n== Test Bio::Sequence::NA#illegal_bases"
!   p na.illegal_bases
!   p Bio::Sequence::NA.new('tacgyrkmhdbvswn').illegal_bases
!   p Bio::Sequence::NA.new('abcdefghijklmnopqrstuvwxyz-!%#$@').illegal_bases
! 
!   puts "\n== Test Bio::Sequence::NA#molecular_weight"
!   p na
!   p na.molecular_weight
!   p rna
!   p rna.molecular_weight
! 
!   puts "\n== Test Bio::Sequence::NA#to_re"
!   p Bio::Sequence::NA.new('atgcrymkdhvbswn')
!   p Bio::Sequence::NA.new('atgcrymkdhvbswn').to_re
!   p Bio::Sequence::NA.new('augcrymkdhvbswn')
!   p Bio::Sequence::NA.new('augcrymkdhvbswn').to_re
! 
!   puts "\n== Test Bio::Sequence::NA#names"
!   p na.names
! 
!   puts "\n== Test Bio::Sequence::NA#pikachu"
!   p na.pikachu
! 
!   puts "\n== Test Bio::Sequence::NA#randomize"
!   print "Orig  : "; p na
!   print "Rand  : "; p na.randomize
!   print "Rand  : "; p na.randomize
!   print "Rand  : "; p na.randomize.randomize
!   print "Block : "; na.randomize do |x| print x end; puts
! 
!   print "Orig  : "; p rna
!   print "Rand  : "; p rna.randomize
!   print "Rand  : "; p rna.randomize
!   print "Rand  : "; p rna.randomize.randomize
!   print "Block : "; rna.randomize do |x| print x end; puts
! 
!   puts "\n== Test Bio::Sequence::NA.randomize(counts)"
!   print "Count : "; p counts = {'a'=>10,'c'=>20,'g'=>30,'t'=>40}
!   print "Rand  : "; p Bio::Sequence::NA.randomize(counts)
!   print "Count : "; p counts = {'a'=>10,'c'=>20,'g'=>30,'u'=>40}
!   print "Rand  : "; p Bio::Sequence::NA.randomize(counts)
!   print "Block : "; Bio::Sequence::NA.randomize(counts) {|x| print x}; puts
! 
!   puts "\n== Test Bio::Sequence::AA#codes"
!   p aa
!   p aa.codes
! 
!   puts "\n== Test Bio::Sequence::AA#names"
!   p aa
!   p aa.names
! 
!   puts "\n== Test Bio::Sequence::AA#molecular_weight"
!   p aa.subseq(1,20)
!   p aa.subseq(1,20).molecular_weight
! 
!   puts "\n== Test Bio::Sequence::AA#randomize"
!   aaseq = 'MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA'
!   s = Bio::Sequence::AA.new(aaseq)
!   print "Orig  : "; p s
!   print "Rand  : "; p s.randomize
!   print "Rand  : "; p s.randomize
!   print "Rand  : "; p s.randomize.randomize
!   print "Block : "; s.randomize {|x| print x}; puts
  
!   puts "\n== Test Bio::Sequence::AA.randomize(counts)"
!   print "Count : "; p counts = s.composition
!   print "Rand  : "; puts Bio::Sequence::AA.randomize(counts)
!   print "Block : "; Bio::Sequence::AA.randomize(counts) {|x| print x}; puts
  
  end
--- 380,404 ----
  if __FILE__ == $0
  
!   require 'bio'
!   seq = Bio::Sequence.new('aattaaaacgccacgcaaggcgattctaggaaatcaaaacgacacgaaatgtggggtgggtgtttgggtaggaaagacagttgtcaacatcagggatttggattgaatcaaaaaaaaagtccttagatttcataaaagctaatcacgcctcaaaactggggcctatctcttcttttttgtcgcttcctgtcggtccttctctatttcttctccaacccctcatttttgaatatttacataacaaaccgttttactttctttggtcaaaattagacccaaaattctatattagtttaagatatgtggtctgtaatttattgttgtattgatataaaaattagttataagcgattatatttttatgctcaagtaactggtgttagttaactatattccaccacgataacctgattacataaaatatgattttaatcattttagtaaaccatatcgcacgttggatgattaattttaacggtttaataacacgtgattaaattatttttagaatgattatttacaaacggaaaagctatatgtgacacaataactcgtgcagtattgttagtttgaaaagtgtatttggtttcttatatttggcctcgattttcagtttatgtgctttttacaaagttttattttcgttatctgtttaacgcgacatttgttgtatggctttaccgatttgagaataaaatcatattacctttatgtagccatgtgtggtgtaatatataataatggtccttctacgaaaaaagcagatcacaattgaaataaagggtgaaatttggtgtcccttttcttcgtcgaaataacagaactaaataaaagaaagtgttatagtatattacgtccgaagaataatccatattcctgaaatacagtcaacatattatatatttagtactttatataaagttaggaattaaatcatatgttttatcgaccatattaagt!
 cacaactttatcataaattaatctgtaattagaattccaagttcgccaccgaatttcgtaacctaatctacatataatagataaaatatatatatgtagagtaattatgatatctatgtatgtagtcatggtatatgaattttgaaattggcaaggtaacattgacggatcgtaacccaacaaataatattaattacaaaatgggtgggcgggaatagtatacaactcataattccactcactttttgtattattaggatatgaaataagagtaatcaacatgcataataaagatgtataatttcttcatcttaaaaaacataactacatggtttaatacacaattttaccttttatcaaaaaagtatttcacaattcactcgcaaattacgaaatgatggctagtgcttcaactccaaatttcgaatattttaaatcacgatgtgtagaaccttttatttactggatactaatcactagtttattgagccaaccaattagttaaatagaacaatcaatattatagccagatattttttcctttaaaaatatttaaaagaggggccagaaaagaaccagagagggaggccatgagacattattatcactagtcaaaaacaacaaaccctccttttgctttttcatataaattattatattttattttgcaggtttcttctcttcttcttcttcttcttcttcttcttcctcttggctgctttctttcatcatccataaagtgaaagctaacgcatagagagagccatatcgtcccaaaaaaagcaaaagtccaaaaaaaaacaactccaaaacattctctcttagctctttactctttagtttctctctctctctctgcctttctctttgttgaagttcatggatgctacgaagtggactcaggtacgtaaaaagatatctctctgctatatctgtttgtttgtagcttctccccgactctcacgctctctctctctctctctctctc!
 tttgtgtatctctctactcacataaatatatacatgtgtgtgtatgcatgtttatatgtatgtatgaaac
cagtagtggttatacagatagtctatatagagatatcaatatgatgtgttttaatttagactttttatatatccgtttgaaacttccgaagttctcgaatggagttaaggaagttttgttctctacaagttcaatttttcttgtcattaattataaaactctgataactaatggataaaaaaggtatgctttgttagttaccttttgttcttggtgctcaggtcttaccatttttttcctaaattttaattagtctcctttctttaattaattttatgttaacgcactgacgatttaacgttaacaaaaaaacctagattctttttcttttcaatagagcataattattacttcaatttcatttatctcacactaaaccctaatcttggcgaaattccttttatatatataaatttaattaatttttccacaatcttggcggaattcaggactcggttttgcttgttattgttctctcttttaatttgacatggttagggaatacttaaagtatgtcttaattttatagggttttcaagaaatgataaacgtaaagccaatggagcaaatgatttctagcaccaacaacaacacaccgcaacaacaaccaacattcatcgccaccaacacaaggccaaacgccaccgcatccaatggtggctccggaggaaataccaacaacacggctacgatggaaactagaaaggcgaggccacaagagaaagtaaattgtccaagatgcaactcaacaaacacaaagttctgttattacaacaactacagtctcacgcaaccaagatacttctgcaaaggttgtcgaaggtattggaccgaaggtggctctcttcgtaacgtcccagtcggaggtagctcaagaaagaacaagagatcctctacacctttagcttcaccttctaatcccaaacttccagatctaaacccaccgattcttttctcaagccaaatccctaataagtcaaataaagatc!
 tcaacttgctatctttcccggtcatgcaagatcatcatcatcatggtatgtctcatttttttcatatgcccaagatagagaacaacaatacttcatcctcaatctatgcttcatcatctcctgtctcagctcttgagcttctaagatccaatggagtctcttcaagaggcatgaacacgttcttgcctggtcaaatgatggattcaaactcagtcctgtactcatctttagggtttccaacaatgcctgattacaaacagagtaataacaacctttcattctccattgatcatcatcaagggattggacataacaccatcaacagtaaccaaagagctcaagataacaatgatgacatgaatggagcaagtagggttttgttccctttttcagacatgaaagagctttcaagcacaacccaagagaagagtcatggtaataatacatattggaatgggatgttcagtaatacaggaggatcttcatggtgaaaaaaggttaaaaagagctcatgaactatcagctttcttctctttttctgtttttttctcctattttattatagtttttactttgatgatcttttgttttttctcacatggggaactttacttaaagttgtcagaacttagtttacagattgtctttttattccttctttctggttttccttttttcctttttttatcagtctttttaaaatatgtatttcataattgggtttgatcattcatatttattagtatcaaaatagagtctatgttcatgagggagtgttaaggggtgtgagggtagaagaataagtgaatacgggggcccg')
!   seq.entry_id = 'AJ224122'
!   seq.sequence_version = 3
!   seq.topology = 'linear'
!   seq.molecule_type = 'genomic DNA'
!   seq.data_class = 'STD'
!   seq.division = 'PLN'
!   seq.primary_accession = 'AJ224122'
!   seq.secondary_accessions = []
!   seq.date_created = '27-FEB-1998 (Rel. 54, Created)'
!   seq.date_modified = '14-NOV-2006 (Rel. 89, Last updated, Version 6)'
!   seq.definition = 'Arabidopsis thaliana DAG1 gene'
!   seq.keywords = ['BBFa gene', 'transcription factor']
!   seq.species = 'Arabidopsis thaliana (thale cress)'
!   seq.classification = ['Eukaryota', 'Viridiplantae', 'Streptophyta', 'Embryophyta', 'Tracheophyta',
!     'Spermatophyta', 'Magnoliophyta', 'eudicotyledons', 'core eudicotyledons', 'rosids',
!     'eurosids II', 'Brassicales', 'Brassicaceae', 'Arabidopsis']
  
! #  puts seq.output(:embl)
!   puts seq.output(:fasta)
  
  end


From ngoto at dev.open-bio.org  Fri Feb 15 00:29:52 2008
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Fri, 15 Feb 2008 05:29:52 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio sequence.rb,0.58.2.5,0.58.2.6
Message-ID: <200802150529.m1F5Tqn1026874@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv26854/lib/bio

Modified Files:
      Tag: BRANCH-biohackathon2008
	sequence.rb 
Log Message:
bugfix in Bio::Sequence.read: mistaken method name


Index: sequence.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence.rb,v
retrieving revision 0.58.2.5
retrieving revision 0.58.2.6
diff -C2 -d -r0.58.2.5 -r0.58.2.6
*** sequence.rb	15 Feb 2008 04:49:37 -0000	0.58.2.5
--- sequence.rb	15 Feb 2008 05:29:50 -0000	0.58.2.6
***************
*** 361,365 ****
        klass = format
      else
!       klass = Bio::FlatFile::AutoDetect.default.guess(str)
      end
      obj = klass.new(str)
--- 361,365 ----
        klass = format
      else
!       klass = Bio::FlatFile::AutoDetect.default.autodetect(str)
      end
      obj = klass.new(str)


From aerts at dev.open-bio.org  Mon Feb 18 10:43:29 2008
From: aerts at dev.open-bio.org (Jan Aerts)
Date: Mon, 18 Feb 2008 15:43:29 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/db/fasta - New directory
Message-ID: <200802181543.m1IFhTLc011233@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/db/fasta
In directory dev.open-bio.org:/tmp/cvs-serv11213/fasta

Log Message:
Directory /home/repository/bioruby/bioruby/lib/bio/db/fasta added to the repository
--> Using per-directory sticky tag `BRANCH-biohackathon2008'



From aerts at dev.open-bio.org  Mon Feb 18 10:44:41 2008
From: aerts at dev.open-bio.org (Jan Aerts)
Date: Mon, 18 Feb 2008 15:44:41 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio reference.rb,1.24,1.24.2.1
Message-ID: <200802181544.m1IFifJc011281@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv11261

Modified Files:
      Tag: BRANCH-biohackathon2008
	reference.rb 
Log Message:
Added export method to EMBL format.


Index: reference.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/reference.rb,v
retrieving revision 1.24
retrieving revision 1.24.2.1
diff -C2 -d -r1.24 -r1.24.2.1
*** reference.rb	5 Apr 2007 23:35:39 -0000	1.24
--- reference.rb	18 Feb 2008 15:44:39 -0000	1.24.2.1
***************
*** 2,8 ****
  # = bio/reference.rb - Journal reference classes
  #
! # Copyright::   Copyright (C) 2001, 2006
  #               Toshiaki Katayama <k at bioruby.org>,
! #               Ryan Raaum <ryan at raaum.org>
  # License::     The Ruby License
  #
--- 2,9 ----
  # = bio/reference.rb - Journal reference classes
  #
! # Copyright::   Copyright (C) 2001, 2006, 2008
  #               Toshiaki Katayama <k at bioruby.org>,
! #               Ryan Raaum <ryan at raaum.org>,
! #               Jan Aerts <jandot at bioruby.org>
  # License::     The Ruby License
  #
***************
*** 79,82 ****
--- 80,89 ----
      # Affiliations in an Array.
      attr_reader :affiliations
+     
+     # Sequence number in EMBL/GenBank records
+     attr_reader :embl_gb_record_number
+     
+     # Position in a sequence that this reference refers to
+     attr_reader :sequence_position
  
      # Create a new Bio::Reference object from a Hash of values. 
***************
*** 130,133 ****
--- 137,144 ----
        @url      = hash['url']
        @mesh     = hash['mesh']
+       @embl_gb_record_number = hash['embl_gb_record_number'] || nil
+       @sequence_position = hash['sequence_position'] || []
+       @comments = hash['comments'] || []
+       @xrefs    = hash['xrefs'] || []
        @affiliations = hash['affiliations']
        @authors = [] if @authors.empty?
***************
*** 171,174 ****
--- 182,187 ----
      def format(style = nil, option = nil)
        case style
+       when 'embl'
+         return embl
        when 'endnote'
          return endnote
***************
*** 246,249 ****
--- 259,298 ----
      end
  
+     # Returns reference formatted in the EMBL style.
+     #
+     #   # ref is a Bio::Reference object
+     #   puts ref.embl
+     #
+     #     RP   1-1859
+     #     RX   PUBMED; 1907511.
+     #     RA   Oxtoby E., Dunn M.A., Pancoro A., Hughes M.A.;
+     #     RT   "Nucleotide and derived amino acid sequence of the cyanogenic
+     #     RT   beta-glucosidase (linamarase) from white clover (Trifolium repens L.)";
+     #     RL   Plant Mol. Biol. 17(2):209-219(1991).
+     def embl
+       lines = Array.new
+       if ! @embl_gb_record_number.nil?
+         lines << "RN   [#{@embl_gb_record_number}]"
+       end
+       if @comments != []
+         @comments.each do |c|
+           lines << "RC   #{c}"
+         end
+       end
+       if @sequence_position != ''
+         lines << "RP   #{@sequence_position}"
+       end
+       if ! @xrefs.nil?
+         @xrefs.each do |x|
+           lines << "RX   #{x}"
+         end
+       end
+       lines << @authors.join(', ').wrap(80, 'RA   ') + ';' unless @authors.nil?
+       lines << (@title == '' ? 'RT   ;' : ('"' + @title + '"').wrap(80, 'RT   ') + ';')
+       lines << @journal.wrap(80, 'RL   ') unless @journal == ''
+       lines << "XX"
+       return lines.join("\n")
+     end
+ 
      # Returns reference formatted in the bibitem style
      #
***************
*** 542,546 ****
    #
    class References
! 
      # Array of Bio::Reference objects
      attr_accessor :references
--- 591,596 ----
    #
    class References
!     include Enumerable
!     
      # Array of Bio::Reference objects
      attr_accessor :references


From k at dev.open-bio.org  Mon Feb 18 22:36:54 2008
From: k at dev.open-bio.org (Katayama Toshiaki)
Date: Tue, 19 Feb 2008 03:36:54 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/io ncbirest.rb, NONE, 1.1 pubmed.rb,
	1.23, 1.24
Message-ID: <200802190336.m1J3as4O012327@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/io
In directory dev.open-bio.org:/tmp/cvs-serv12321

Modified Files:
	pubmed.rb 
Added Files:
	ncbirest.rb 
Log Message:
* NCBI E-Utilities (REST) functionality is separated to ncbirest.rb
  and pubmed.rb is changed to utilize the Bio::NCBI::REST class for
  esearch and efetch. You can now search and retrieve any database
  in any format that NCBI supports by E-Utilities through the
  Bio::NCBI::REST interface (currently, only esearch and efetch methods
  are implemented).


Index: pubmed.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/pubmed.rb,v
retrieving revision 1.23
retrieving revision 1.24
diff -C2 -d -r1.23 -r1.24
*** pubmed.rb	12 Dec 2007 13:53:26 -0000	1.23
--- pubmed.rb	19 Feb 2008 03:36:52 -0000	1.24
***************
*** 2,6 ****
  # = bio/io/pubmed.rb - NCBI Entrez/PubMed client module
  #
! # Copyright::  Copyright (C) 2001, 2007 Toshiaki Katayama <k at bioruby.org>
  # Copyright::  Copyright (C) 2006 Jan Aerts <jan.aerts at bbsrc.ac.uk>
  # License::    The Ruby License
--- 2,6 ----
  # = bio/io/pubmed.rb - NCBI Entrez/PubMed client module
  #
! # Copyright::  Copyright (C) 2001, 2007, 2008 Toshiaki Katayama <k at bioruby.org>
  # Copyright::  Copyright (C) 2006 Jan Aerts <jan.aerts at bbsrc.ac.uk>
  # License::    The Ruby License
***************
*** 9,12 ****
--- 9,13 ----
  #
  
+ require 'bio/io/ncbirest'
  require 'bio/command'
  require 'cgi' unless defined?(CGI)
***************
*** 69,95 ****
  #   medline = Bio::MEDLINE.new(manuscript)
  #  
! class PubMed
! 
!   # Run retrieval scripts on weekends or between 9 pm and 5 am Eastern Time
!   # weekdays for any series of more than 100 requests.
!   # -> Not implemented yet in BioRuby
! 
!   # Make no more than one request every 3 seconds.
!   NCBI_INTERVAL = 3
!   @@last_access = nil
! 
!   private
! 
!   def ncbi_access_wait(wait = NCBI_INTERVAL)
!     if @@last_access
!       duration = Time.now - @@last_access
!       if wait > duration
!         sleep wait - duration
!       end
!     end
!     @@last_access = Time.now
!   end
! 
!   public
  
    # Search the PubMed database by given keywords using E-Utils and returns 
--- 70,74 ----
  #   medline = Bio::MEDLINE.new(manuscript)
  #  
! class PubMed < Bio::NCBI::REST
  
    # Search the PubMed database by given keywords using E-Utils and returns 
***************
*** 100,136 ****
    # ---
    # *Arguments*:
!   # * _id_: query string (required)
!   # * _field_
!   # * _reldate_
!   # * _mindate_
!   # * _maxdate_
!   # * _datetype_
!   # * _retstart_
!   # * _retmax_ (default 100)
!   # * _retmode_
!   # * _rettype_
    # *Returns*:: array of PubMed IDs or a number of results
    def esearch(str, hash = {})
!     return nil if str.empty?
! 
!     serv = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"
!     opts = {
!       "retmax" => 100,
!       "tool"   => "bioruby",
!       "db"     => "pubmed",
!       "term"   => str
!     }
      opts.update(hash)
! 
!     ncbi_access_wait
! 
!     response, = Bio::Command.post_form(serv, opts)
!     result = response.body
!     if opts['rettype'] == 'count'
!       result = result.scan(/<Count>(.*?)<\/Count>/m).flatten.first.to_i
!     else
!       result = result.scan(/<Id>(.*?)<\/Id>/m).flatten
!     end
!     return result
    end
  
--- 79,98 ----
    # ---
    # *Arguments*:
!   # * _str_: query string (required)
!   # * _hash_: hash of E-Utils options
!   #   * _retmode_: "xml", "html", ...
!   #   * _rettype_: "medline", ...
!   #   * _retmax_: integer (default 100)
!   #   * _retstart_: integer
!   #   * _field_
!   #   * _reldate_
!   #   * _mindate_
!   #   * _maxdate_
!   #   * _datetype_
    # *Returns*:: array of PubMed IDs or a number of results
    def esearch(str, hash = {})
!     opts = { "db" => "pubmed" }
      opts.update(hash)
!     super(str, opts)
    end
  
***************
*** 142,168 ****
    # *Arguments*:
    # * _ids_: list of PubMed IDs (required)
    # *Returns*:: Array of MEDLINE formatted String
    def efetch(ids, hash = {})
!     return nil if ids.to_s.empty?
!     ids = ids.join(",") if ids === Array
! 
!     serv = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi"
!     opts = {
!       "tool"     => "bioruby",
!       "db"       => "pubmed",
!       "retmode"  => "text",
!       "rettype"  => "medline",
!       "id"       => ids,
!     }
      opts.update(hash)
! 
!     ncbi_access_wait
! 
!     response, = Bio::Command.post_form(serv, opts)
!     result = response.body
!     if opts["retmode"] == "text"
!       result = result.split(/\n\n+/)
!     end
!     return result
    end
  
--- 104,122 ----
    # *Arguments*:
    # * _ids_: list of PubMed IDs (required)
+   # * _hash_: hash of E-Utils options
+   #   * _retmode_: "xml", "html", ...
+   #   * _rettype_: "medline", ...
+   #   * _retmax_: integer (default 100)
+   #   * _retstart_: integer
+   #   * _field_
+   #   * _reldate_
+   #   * _mindate_
+   #   * _maxdate_
+   #   * _datetype_
    # *Returns*:: Array of MEDLINE formatted String
    def efetch(ids, hash = {})
!     opts = { "db" => "pubmed", "rettype"  => "medline" }
      opts.update(hash)
!     super(ids, opts)
    end
  

--- NEW FILE: ncbirest.rb ---
#
# = bio/io/ncbrest.rb - NCBI Entrez client module
#
# Copyright::  Copyright (C) 2008 Toshiaki Katayama <k at bioruby.org>
# License::    The Ruby License
#
# $Id: ncbirest.rb,v 1.1 2008/02/19 03:36:52 k Exp $
#

require 'bio/command'

module Bio

# == Description
#
# The Bio::NCBI::REST class provides REST client for the NCBI E-Utilities
#
# * Entrez utilities index:
#      http://www.ncbi.nlm.nih.gov/entrez/utils/utils_index.html
# * How to link:
#     http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helplinks.chapter.linkshelp
#
# == Usage
#
#  Bio::NCBI::REST.esearch("tardigrada", {"db"=>"nuccore", "rettype"=>"gb"})
#  Bio::NCBI::REST.esearch("yeast kinase", {"db"=>"nuccore", "rettype"=>"gb", "retmode"=>"xml", "retmax"=>5})
#  Bio::NCBI::REST.efetch("185041", {"db"=>"nuccore", "rettype"=>"gb"})
#  Bio::NCBI::REST.efetch("J00231", {"db"=>"nuccore", "rettype"=>"gb", "retmode"=>"xml"})
#  
class NCBI
class REST

  # Run retrieval scripts on weekends or between 9 pm and 5 am Eastern Time
  # weekdays for any series of more than 100 requests.
  # -> Not implemented yet in BioRuby

  # Make no more than one request every 3 seconds.
  NCBI_INTERVAL = 3
  @@last_access = nil

  private

  def ncbi_access_wait(wait = NCBI_INTERVAL)
    if @@last_access
      duration = Time.now - @@last_access
      if wait > duration
        sleep wait - duration
      end
    end
    @@last_access = Time.now
  end

  public

  # Search the NCBI database by given keywords using E-Utils and returns 
  # an array of entry IDs.
  # 
  # For information on the possible arguments, see
  #
  # * http://eutils.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html
  #
  # ---
  # *Arguments*:
  # * _str_: query string (required)
  # * _hash_: hash of E-Utils option {"db" => "nuccore", "rettype" => "gb"}
  #   * _db_: "nuccore", "pubmed", ...
  #   * _retmode_: "xml", "html", ...
  #   * _rettype_: "gb", "medline", "count", ...
  #   * _retmax_: integer (default 100)
  #   * _retstart_: integer
  #   * _field_
  #   * _reldate_
  #   * _mindate_
  #   * _maxdate_
  #   * _datetype_
  # *Returns*:: array of entry IDs or a number of results
  def esearch(str, hash = {})
    return nil if str.empty?

    serv = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"
    opts = {
      "retmax" => 100,
      "tool"   => "bioruby",
      "term"   => str
    }
    opts.update(hash)

    ncbi_access_wait

    response, = Bio::Command.post_form(serv, opts)
    result = response.body
    if opts['rettype'] == 'count'
      result = result.scan(/<Count>(.*?)<\/Count>/m).flatten.first.to_i
    else
      result = result.scan(/<Id>(.*?)<\/Id>/m).flatten
    end
    return result
  end

  # Retrieve a database entry by given ID and using E-Utils (efetch) and
  # returns an array of entry string. Multiple IDs can be supplied.
  # ---
  # *Arguments*:
  # * _ids_: list of NCBI entry IDs (required)
  # * _hash_: hash of E-Utils option {"db" => "nuccore", "rettype" => "gb"}
  #   * _db_: "nuccore", "pubmed", ...
  #   * _retmode_: "xml", "html", ...
  #   * _rettype_: "gb", "medline", "count",...
  #   * _retmax_: integer (default 100)
  #   * _retstart_: integer
  #   * _field_
  #   * _reldate_
  #   * _mindate_
  #   * _maxdate_
  #   * _datetype_
  # *Returns*:: Array of entry String
  def efetch(ids, hash = {})
    return nil if ids.to_s.empty?
    ids = ids.join(",") if ids === Array

    serv = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi"
    opts = {
      "tool"     => "bioruby",
      "retmode"  => "text",
      "id"       => ids,
    }
    opts.update(hash)

    ncbi_access_wait

    response, = Bio::Command.post_form(serv, opts)
    result = response.body
    if opts["retmode"] == "text"
      result = result.split(/\n\n+/)
    end
    return result
  end

  def self.esearch(*args)
    self.new.esearch(*args)
  end

  def self.efetch(*args)
    self.new.efetch(*args)
  end

end # REST
end # NCBI
end # Bio


if __FILE__ == $0

  gbopts = {"db"=>"nuccore", "rettype"=>"gb"}
  pmopts = {"db"=>"pubmed", "rettype"=>"medline"}
  count = {"rettype" => "count"}
  xml = {"retmode"=>"xml"}
  max = {"retmax"=>5}

  puts "=== class methods ==="

  puts "--- Search NCBI by E-Utils ---"

  puts Time.now
  puts "# count of 'tardigrada' in nuccore"
  puts Bio::NCBI::REST.esearch("tardigrada", gbopts.merge(count))

  puts Time.now
  puts "# max 5 'tardigrada' entries in nuccore"
  puts Bio::NCBI::REST.esearch("tardigrada", gbopts.merge(max))

  puts Time.now
  puts "# count of 'yeast kinase' in nuccore"
  puts Bio::NCBI::REST.esearch("yeast kinase", gbopts.merge(count))

  puts Time.now
  puts "# max 5 'yeast kinase' entries in nuccore (XML)"
  puts Bio::NCBI::REST.esearch("yeast kinase", gbopts.merge(xml).merge(max))

  puts Time.now
  puts "# count of 'genome&analysis|bioinformatics' in pubmed"
  puts Bio::NCBI::REST.esearch("(genome AND analysis) OR bioinformatics", pmopts.merge(count))

  puts Time.now
  puts "# max 5 'genome&analysis|bioinformatics' entries in pubmed (XML)"
  puts Bio::NCBI::REST.esearch("(genome AND analysis) OR bioinformatics", pmopts.merge(xml).merge(max))

  puts Time.now
  Bio::NCBI::REST.esearch("(genome AND analysis) OR bioinformatics", pmopts.merge(max)).each do |x|
    puts "# each of 5 'genome&analysis|bioinformatics' entries in pubmed"
    puts x
  end

  puts "--- Retrieve NCBI entry by E-Utils ---"

  puts Time.now
  puts "# '185041' entry in nuccore"
  puts Bio::NCBI::REST.efetch("185041", gbopts)

  puts Time.now
  puts "# 'J00231' entry in nuccore (XML)"
  puts Bio::NCBI::REST.efetch("J00231", gbopts.merge(xml))

  puts Time.now
  puts "# 16381885 entry in pubmed"
  puts Bio::NCBI::REST.efetch(16381885, pmopts)

  puts Time.now
  puts "# '16381885' entry in pubmed"
  puts Bio::NCBI::REST.efetch("16381885", pmopts)

  puts Time.now
  puts "# [10592173,14693808] entries in pubmed"
  puts Bio::NCBI::REST.efetch([10592173, 14693808], pmopts)

  puts Time.now
  puts "# [10592173,14693808] entries in pubmed (XML)"
  puts Bio::NCBI::REST.efetch([10592173, 14693808], pmopts.merge(xml))


  puts "=== instance methods ==="

  ncbi = Bio::NCBI::REST.new

  puts "--- Search NCBI by E-Utils ---"

  puts Time.now
  puts "# count of 'genome&analysis|bioinformatics' in pubmed"
  puts ncbi.esearch("(genome AND analysis) OR bioinformatics", pmopts.merge(count))

  puts Time.now
  puts "# max 5 'genome&analysis|bioinformatics' entries in pubmed"
  puts ncbi.esearch("(genome AND analysis) OR bioinformatics", pmopts.merge(max))

  puts Time.now
  ncbi.esearch("(genome AND analysis) OR bioinformatics", pmopts).each do |x|
    puts "# each 'genome&analysis|bioinformatics' entries in pubmed"
    puts x
  end

  puts "--- Retrieve NCBI entry by E-Utils ---"

  puts Time.now
  puts "# 16381885 entry in pubmed"
  puts ncbi.efetch(16381885, pmopts)

  puts Time.now
  puts "# [10592173,14693808] entries in pubmed"
  puts ncbi.efetch([10592173, 14693808], pmopts)

end


From k at dev.open-bio.org  Mon Feb 18 23:42:16 2008
From: k at dev.open-bio.org (Katayama Toshiaki)
Date: Tue, 19 Feb 2008 04:42:16 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/io hinv.rb,1.1,1.2
Message-ID: <200802190442.m1J4gGQZ012425@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/io
In directory dev.open-bio.org:/tmp/cvs-serv12421

Modified Files:
	hinv.rb 
Log Message:
* hit2acc fixed


Index: hinv.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/hinv.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** hinv.rb	9 Jan 2008 17:18:18 -0000	1.1
--- hinv.rb	19 Feb 2008 04:42:14 -0000	1.2
***************
*** 2,6 ****
  # = bio/io/hinv.rb - H-invDB web service (REST) client module
  #
! # Copyright::  Copyright (C) 2007 Toshiaki Katayama <k at bioruby.org>
  # License::    The Ruby License
  #
--- 2,6 ----
  # = bio/io/hinv.rb - H-invDB web service (REST) client module
  #
! # Copyright::  Copyright (C) 2008 Toshiaki Katayama <k at bioruby.org>
  # License::    The Ruby License
  #
***************
*** 137,141 ****
  
        def initialize
!         @url = BASE_URI + "hit2acc.php?hit="
        end
  
--- 137,141 ----
  
        def initialize
!         @url = BASE_URI + "hit2acc.php"
        end
  


From k at dev.open-bio.org  Mon Feb 18 23:49:37 2008
From: k at dev.open-bio.org (Katayama Toshiaki)
Date: Tue, 19 Feb 2008 04:49:37 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/io ncbirest.rb,1.1,1.2
Message-ID: <200802190449.m1J4nb9x012447@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/io
In directory dev.open-bio.org:/tmp/cvs-serv12443

Modified Files:
	ncbirest.rb 
Log Message:
* doc update


Index: ncbirest.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/ncbirest.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** ncbirest.rb	19 Feb 2008 03:36:52 -0000	1.1
--- ncbirest.rb	19 Feb 2008 04:49:35 -0000	1.2
***************
*** 1,4 ****
  #
! # = bio/io/ncbrest.rb - NCBI Entrez client module
  #
  # Copyright::  Copyright (C) 2008 Toshiaki Katayama <k at bioruby.org>
--- 1,4 ----
  #
! # = bio/io/ncbirest.rb - NCBI Entrez client module
  #
  # Copyright::  Copyright (C) 2008 Toshiaki Katayama <k at bioruby.org>
***************
*** 16,26 ****
  # The Bio::NCBI::REST class provides REST client for the NCBI E-Utilities
  #
! # * Entrez utilities index:
! #      http://www.ncbi.nlm.nih.gov/entrez/utils/utils_index.html
! # * How to link:
! #     http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helplinks.chapter.linkshelp
  #
  # == Usage
  #
  #  Bio::NCBI::REST.esearch("tardigrada", {"db"=>"nuccore", "rettype"=>"gb"})
  #  Bio::NCBI::REST.esearch("yeast kinase", {"db"=>"nuccore", "rettype"=>"gb", "retmode"=>"xml", "retmax"=>5})
--- 16,26 ----
  # The Bio::NCBI::REST class provides REST client for the NCBI E-Utilities
  #
! # Entrez utilities index:
! #
! # * http://www.ncbi.nlm.nih.gov/entrez/utils/utils_index.html
  #
  # == Usage
  #
+ #  Bio::NCBI::REST.esearch("tardigrada", {"db"=>"nuccore", "rettype"=>"count"})
  #  Bio::NCBI::REST.esearch("tardigrada", {"db"=>"nuccore", "rettype"=>"gb"})
  #  Bio::NCBI::REST.esearch("yeast kinase", {"db"=>"nuccore", "rettype"=>"gb", "retmode"=>"xml", "retmax"=>5})
***************
*** 64,69 ****
    # * _str_: query string (required)
    # * _hash_: hash of E-Utils option {"db" => "nuccore", "rettype" => "gb"}
!   #   * _db_: "nuccore", "pubmed", ...
!   #   * _retmode_: "xml", "html", ...
    #   * _rettype_: "gb", "medline", "count", ...
    #   * _retmax_: integer (default 100)
--- 64,69 ----
    # * _str_: query string (required)
    # * _hash_: hash of E-Utils option {"db" => "nuccore", "rettype" => "gb"}
!   #   * _db_: "nuccore", "nucleotide", "protein", "pubmed", ...
!   #   * _retmode_: "text", "xml", "html", ...
    #   * _rettype_: "gb", "medline", "count", ...
    #   * _retmax_: integer (default 100)
***************
*** 100,109 ****
    # Retrieve a database entry by given ID and using E-Utils (efetch) and
    # returns an array of entry string. Multiple IDs can be supplied.
    # ---
    # *Arguments*:
    # * _ids_: list of NCBI entry IDs (required)
    # * _hash_: hash of E-Utils option {"db" => "nuccore", "rettype" => "gb"}
!   #   * _db_: "nuccore", "pubmed", ...
!   #   * _retmode_: "xml", "html", ...
    #   * _rettype_: "gb", "medline", "count",...
    #   * _retmax_: integer (default 100)
--- 100,114 ----
    # Retrieve a database entry by given ID and using E-Utils (efetch) and
    # returns an array of entry string. Multiple IDs can be supplied.
+   #
+   # For information on the possible arguments, see
+   #
+   # * http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetch_help.html
+   #
    # ---
    # *Arguments*:
    # * _ids_: list of NCBI entry IDs (required)
    # * _hash_: hash of E-Utils option {"db" => "nuccore", "rettype" => "gb"}
!   #   * _db_: "nuccore", "nucleotide", "protein", "pubmed", ...
!   #   * _retmode_: "text", "xml", "html", ...
    #   * _rettype_: "gb", "medline", "count",...
    #   * _retmax_: integer (default 100)


From aerts at dev.open-bio.org  Wed Feb 20 04:56:24 2008
From: aerts at dev.open-bio.org (Jan Aerts)
Date: Wed, 20 Feb 2008 09:56:24 +0000
Subject: [BioRuby-cvs] bioruby ChangeLog,1.83,1.83.2.1
Message-ID: <200802200956.m1K9uOcm015785@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby
In directory dev.open-bio.org:/tmp/cvs-serv15755

Modified Files:
      Tag: BRANCH-biohackathon2008
	ChangeLog 
Log Message:
* Rewrote some of the code for converting EMBL files into Bio::Sequence.
* Added functionality to export Bio::Sequence to EMBL format.

Changes:
* renamed Sequence::Format#wrap and #fold to String#wrap and #fold (stored in bio.rb)
* lib/bio/db/common.rb:
    - rewrote def ref and def references
    - added to_biosequence
    - def references now returns an Array instead of a Bio::References object (tests changed accordingly)
* lib/bio/db/embl/embl.rb
    - def ft now returns Array instead of Bio::Features object (tests changed accordingly)
* lib/bio/db/embl/format.erb
* lib/bio/sequence/common.rb
    - added def format_embl


Index: ChangeLog
===================================================================
RCS file: /home/repository/bioruby/bioruby/ChangeLog,v
retrieving revision 1.83
retrieving revision 1.83.2.1
diff -C2 -d -r1.83 -r1.83.2.1
*** ChangeLog	12 Feb 2008 05:32:23 -0000	1.83
--- ChangeLog	20 Feb 2008 09:56:21 -0000	1.83.2.1
***************
*** 1,2 ****
--- 1,27 ----
+ 2008-02-20  Jan Aerts <jandot at bioruby.org>
+         * lib/bio/db/fasta.rb
+         * lib/bio/db/fasta/format.erb
+         * test/unit/bio/db/test_fasta.rb
+ 
+           Renamed #to_seq to #to_biosequence to reflect that same method in
+           embl.rb, genbank.rb and others.
+ 
+ 2008-02-20  Jan Aerts <jandot at bioruby.org>
+         * lib/bio.rb
+         * lib/bio/db/embl/common.rb
+         * lib/bio/db/embl/embl.rb
+         * lib/bio/db/embl/format.erb
+         * lib/bio/sequence/common.rb
+         * lib/bio/sequence/format.rb
+         * test/unit/bio/db/embl/test_embl_to_bioseq.rb
+ 
+         Fixed some bugs in importing EMBL files and added functionality to
+         export a Bio::Sequence to EMBL format.
+ 
+ 2008-02-18  Jan Aerts <jandot at bioruby.org>
+         * lib/bio/reference.rb
+ 
+           Added export method to EMBL format.
+ 
  2008-02-12  Naohisa Goto <ng at bioruby.org>
  


From aerts at dev.open-bio.org  Wed Feb 20 04:56:24 2008
From: aerts at dev.open-bio.org (Jan Aerts)
Date: Wed, 20 Feb 2008 09:56:24 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/db/embl format.erb, NONE,
	1.1.2.1 common.rb, 1.12, 1.12.2.1 embl.rb, 1.29.2.1, 1.29.2.2
Message-ID: <200802200956.m1K9uO6r015800@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/db/embl
In directory dev.open-bio.org:/tmp/cvs-serv15755/lib/bio/db/embl

Modified Files:
      Tag: BRANCH-biohackathon2008
	common.rb embl.rb 
Added Files:
      Tag: BRANCH-biohackathon2008
	format.erb 
Log Message:
* Rewrote some of the code for converting EMBL files into Bio::Sequence.
* Added functionality to export Bio::Sequence to EMBL format.

Changes:
* renamed Sequence::Format#wrap and #fold to String#wrap and #fold (stored in bio.rb)
* lib/bio/db/common.rb:
    - rewrote def ref and def references
    - added to_biosequence
    - def references now returns an Array instead of a Bio::References object (tests changed accordingly)
* lib/bio/db/embl/embl.rb
    - def ft now returns Array instead of Bio::Features object (tests changed accordingly)
* lib/bio/db/embl/format.erb
* lib/bio/sequence/common.rb
    - added def format_embl


--- NEW FILE: format.erb ---
ID   <%= entry_id %>; SV <%= sequence_version %>; <%= topology %>; <%= molecule_type %>; <%= data_class %>; <%= division %>; <%= seq.length %> BP.
XX
AC   <%= accessions.reject{|a| a.nil?}.join('; ') + ';' %>
XX
DT   <%= date_created %>
DT   <%= date_modified %>
XX
DE   <%= definition %>
XX
KW   <%= keywords.join('; ') %>.
XX
OS   <%= species %>
<%= classification.join('; ').wrap(80, 'OC   ') %>.
XX   
<%= references.collect{|ref| ref.format('embl')}.join("\n") %>
XX
FH   Key             Location/Qualifiers
FH
<%  prefix = 'FT   '
    indent = prefix + ' ' * 16
    fwidth = 80 - indent.length %><%= format_features(prefix, indent, fwidth) %>XX
SQ   Sequence <%= seq.length %> BP; <%= seq.composition.collect{|k,v| "#{v} #{k.upcase}"}.join('; ') + '; ' + (seq.gsub(/[ACTGactg]/, '').length.to_s ) + ' other;' %>
<%= seq.format_embl %>
//
Index: embl.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/embl.rb,v
retrieving revision 1.29.2.1
retrieving revision 1.29.2.2
diff -C2 -d -r1.29.2.1 -r1.29.2.2
*** embl.rb	15 Feb 2008 04:49:37 -0000	1.29.2.1
--- embl.rb	20 Feb 2008 09:56:22 -0000	1.29.2.2
***************
*** 123,126 ****
--- 123,130 ----
    alias molecule_type molecule
  
+   def data_class
+     id_line('DATA_CLASS')
+   end
+   
    def topology
      id_line('TOPOLOGY')
***************
*** 254,258 ****
      unless @data['FT']
        @data['FT'] = Array.new
-       ary = Array.new
        in_quote = false
        @orig['FT'].each_line do |line|
--- 258,261 ----
***************
*** 262,268 ****
          body = line[20,60].chomp # feature value (position, /qualifier=)
          if line =~ /^FT {3}(\S+)/
!           ary.push([ $1, body ]) # [ feature, position, /q="data", ... ]
          elsif body =~ /^ \// and not in_quote
!           ary.last.push(body)    # /q="data..., /q=data, /q
  
            if body =~ /=" / and body !~ /"$/
--- 265,271 ----
          body = line[20,60].chomp # feature value (position, /qualifier=)
          if line =~ /^FT {3}(\S+)/
!           @data['FT'].push([ $1, body ]) # [ feature, position, /q="data", ... ]
          elsif body =~ /^ \// and not in_quote
!           @data['FT'].last.push(body)    # /q="data..., /q=data, /q
  
            if body =~ /=" / and body !~ /"$/
***************
*** 271,275 ****
  
          else
!           ary.last.last << body # ...data..., ...data..."
  
            if body =~ /"$/
--- 274,278 ----
  
          else
!           @data['FT'].last.last << body # ...data..., ...data..."
  
            if body =~ /"$/
***************
*** 279,287 ****
        end
  
!       ary.map! do |subary|
          parse_qualifiers(subary)
        end
  
-       @data['FT'] = Features.new(ary)
      end
      if block_given?
--- 282,289 ----
        end
  
!       @data['FT'].map! do |subary|
          parse_qualifiers(subary)
        end
  
      end
      if block_given?
***************
*** 373,378 ****
      bio_seq.entry_id = self.entry_id
      bio_seq.primary_accession = self.accessions[0]
!     bio_seq.secondary_accessions = self.accessions[1,-1]
      bio_seq.molecule_type = self.molecule_type
      bio_seq.definition = self.description
      bio_seq.topology = self.topology
--- 375,381 ----
      bio_seq.entry_id = self.entry_id
      bio_seq.primary_accession = self.accessions[0]
!     bio_seq.secondary_accessions = self.accessions[1,-1] || []
      bio_seq.molecule_type = self.molecule_type
+     bio_seq.data_class = self.data_class
      bio_seq.definition = self.description
      bio_seq.topology = self.topology
***************
*** 382,386 ****
      bio_seq.sequence_version = self.version
      bio_seq.keywords = self.keywords
!     bio_seq.species = self.os(0)[0]['os'] + ' ' + self.os(0)[0]['name']
      bio_seq.classification = self.oc
      bio_seq.references = self.references
--- 385,389 ----
      bio_seq.sequence_version = self.version
      bio_seq.keywords = self.keywords
!     bio_seq.species = self.fetch('OS')
      bio_seq.classification = self.oc
      bio_seq.references = self.references
***************
*** 435,439 ****
    indent = prefix + ' ' * 16
    fwidth = 80 - indent.length
!   
    parser = Bio::FlatFile.auto('/home/aertsj/LocalDocuments/hackathon/aj224122.embl')
    parser.each do |entry|
--- 438,443 ----
    indent = prefix + ' ' * 16
    fwidth = 80 - indent.length
! 
! #  parser = Bio::FlatFile.auto('/home/aertsj/LocalDocuments/bioruby_biohackathon/bioruby/test/data/embl/AB090716.embl')
    parser = Bio::FlatFile.auto('/home/aertsj/LocalDocuments/hackathon/aj224122.embl')
    parser.each do |entry|

Index: common.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/common.rb,v
retrieving revision 1.12
retrieving revision 1.12.2.1
diff -C2 -d -r1.12 -r1.12.2.1
*** common.rb	5 Apr 2007 23:35:40 -0000	1.12
--- common.rb	20 Feb 2008 09:56:22 -0000	1.12.2.1
***************
*** 241,265 ****
    def ref
      unless @data['R']
!       ary = Array.new
!       get('R').split(/\nRN   /).each do |str|
!         raw = {'RN' => '', 'RC' => '', 'RP' => '', 'RX' => '', 
!                'RA' => '', 'RT' => '', 'RL' => '', 'RG' => ''}
!         str = 'RN   ' + str unless /^RN   / =~ str
!         str.split("\n").each do |line|
!           if /^(R[NPXARLCTG])   (.+)/ =~ line
!             raw[$1] += $2 + ' '
!           else
!             raise "Invalid format in R lines, \n[#{line}]\n"
            end
          end
!         raw.each_value {|v| 
!           v.strip! 
!           v.sub!(/^"/,'')
!           v.sub!(/;$/,'')
!           v.sub!(/"$/,'')
!         }
!         ary.push(raw)
        end
-       @data['R'] = ary
      end
      @data['R']
--- 241,305 ----
    def ref
      unless @data['R']
!       @data['R'] = Array.new
!       # Get the different references as 'blurbs' (the lines together)
!       reference_blurbs = get('R').split(/\nRN   /)
!       reference_blurbs.each_index do |i|
!         reference_blurbs[i] = 'RN   ' + reference_blurbs[i] unless reference_blurbs[i] =~ /^RN   /
!       end
!       
!       # For each reference, we'll first create a hash that looks like below.
!       # Suppose the input is:
!       #   RA   name1, name2, name3
!       #   RA   name4
!       #   RT   some part of the title that
!       #   RT   did not fit on one line
!       # Then the hash looks like:
!       #   h = {
!       #         'RA' => ["name1, name2, name3", "name4"],
!       #         'RT' => ["some part of the title that", "did not fit on one line"]
!       #       }
!       reference_blurbs.each do |rb|
!         line_based_data = Hash.new
!         rb.split(/\n/).each do |line|
!           key, value = line.scan(/^(R[A-Z])   "?(\[?.*[A-Za-z0-9]\]?)/)[0]
!           if line_based_data[key].nil?
!             line_based_data[key] = Array.new
            end
+           line_based_data[key].push(value)
          end
! 
!         # Now we have to sanitize the hash: the authors should be kept in an 
!         # array, the title should be 1 string, ... So the hash should look like:
!         #  h = {
!         #        'RA' => ["name1", "name2", "name3", "name4"],
!         #        'RT' => 'some part of the title that did not fit on one line'
!         #      }
!         line_based_data.keys.each do |key|
!           if ['RC', 'RP', 'RT', 'RL'].include?(key)
!             line_based_data[key] = line_based_data[key].join(' ')
!           elsif ['RA', 'RX'].include?(key)
!             sanitized_data = Array.new
!             line_based_data[key].each do |v|
!               sanitized_data.push(v.split(/\s*,\s*/))
!             end
!             line_based_data[key] = sanitized_data.flatten
!           elsif key == 'RN'
!             line_based_data[key] = line_based_data[key][0].sub(/^\[/,'').sub(/\]$/,'').to_i
!           end
!         end
!         
!         # And put it in @data. @data in the end looks like this:
!         #  data = [
!         #           {
!         #             'RA' => ["name1", "name2", "name3", "name4"],
!         #             'RT' => 'some part of the title that did not fit on one line'
!         #           },
!         #           {
!         #             'RA' => ["name1", "name2", "name3", "name4"],
!         #             'RT' => 'some part of the title that did not fit on one line'
!         #           }
!         #         ]
!         @data['R'].push(line_based_data)
        end
      end
      @data['R']
***************
*** 270,306 ****
    def references
      unless @data['references']
!       ary = self.ref.map {|ent|
!         hash = Hash.new('')
!         ent.each {|key, value|
            case key
            when 'RA'
!             hash['authors'] = value.split(/, /)
            when 'RT'
              hash['title'] = value
            when 'RL'
!             if value =~ /(.*) (\d+) \((\d+)\), (\d+-\d+) \((\d+)\)$/
!               hash['journal'] = $1
!               hash['volume']  = $2
!               hash['issue']   = $3
!               hash['pages']   = $4
!               hash['year']    = $5
!             else
!               hash['journal'] = value
!             end
            when 'RX'  # PUBMED, MEDLINE
!             value.split('.').each {|item|
                tag, xref = item.split(/; /).map {|i| i.strip }
                hash[ tag.downcase ]  = xref
              }
            end
!         }
!         Reference.new(hash)
!       }
!       @data['references'] = References.new(ary)
      end
      @data['references']
    end
  
- 
    # returns contents in the DR line.
    # * Bio::EMBLDB::Common#dr  -> [ <Database cross-reference Hash>* ]
--- 310,345 ----
    def references
      unless @data['references']
!       @data['references'] = Array.new
!       self.ref.each do |ref|
!         hash = Hash.new
!         ref.each do |key, value|
            case key
+           when 'RN'
+             hash['embl_gb_record_number'] = value
+           when 'RC'
+             hash['comments'] = value
+           when 'RX'
+             hash['xrefs'] = value
+           when 'RP'
+             hash['sequence_position'] = value
            when 'RA'
!             hash['authors'] = value
            when 'RT'
              hash['title'] = value
            when 'RL'
!             hash['journal'] = value
            when 'RX'  # PUBMED, MEDLINE
!             value.each {|item|
                tag, xref = item.split(/; /).map {|i| i.strip }
                hash[ tag.downcase ]  = xref
              }
            end
!         end
!         @data['references'].push(Reference.new(hash))
!       end
      end
      @data['references']
    end
  
    # returns contents in the DR line.
    # * Bio::EMBLDB::Common#dr  -> [ <Database cross-reference Hash>* ]


From aerts at dev.open-bio.org  Wed Feb 20 04:56:24 2008
From: aerts at dev.open-bio.org (Jan Aerts)
Date: Wed, 20 Feb 2008 09:56:24 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio sequence.rb,0.58.2.6,0.58.2.7
Message-ID: <200802200956.m1K9uO8C015795@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv15755/lib/bio

Modified Files:
      Tag: BRANCH-biohackathon2008
	sequence.rb 
Log Message:
* Rewrote some of the code for converting EMBL files into Bio::Sequence.
* Added functionality to export Bio::Sequence to EMBL format.

Changes:
* renamed Sequence::Format#wrap and #fold to String#wrap and #fold (stored in bio.rb)
* lib/bio/db/common.rb:
    - rewrote def ref and def references
    - added to_biosequence
    - def references now returns an Array instead of a Bio::References object (tests changed accordingly)
* lib/bio/db/embl/embl.rb
    - def ft now returns Array instead of Bio::Features object (tests changed accordingly)
* lib/bio/db/embl/format.erb
* lib/bio/sequence/common.rb
    - added def format_embl


Index: sequence.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence.rb,v
retrieving revision 0.58.2.6
retrieving revision 0.58.2.7
diff -C2 -d -r0.58.2.6 -r0.58.2.7
*** sequence.rb	15 Feb 2008 05:29:50 -0000	0.58.2.6
--- sequence.rb	20 Feb 2008 09:56:22 -0000	0.58.2.7
***************
*** 371,375 ****
      return [@primary_accession, @secondary_accessions].flatten
    end
!   
  end # Sequence
  
--- 371,375 ----
      return [@primary_accession, @secondary_accessions].flatten
    end
! 
  end # Sequence
  


From aerts at dev.open-bio.org  Wed Feb 20 04:56:24 2008
From: aerts at dev.open-bio.org (Jan Aerts)
Date: Wed, 20 Feb 2008 09:56:24 +0000
Subject: [BioRuby-cvs] bioruby/lib bio.rb,1.89,1.89.2.1
Message-ID: <200802200956.m1K9uOdN015790@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib
In directory dev.open-bio.org:/tmp/cvs-serv15755/lib

Modified Files:
      Tag: BRANCH-biohackathon2008
	bio.rb 
Log Message:
* Rewrote some of the code for converting EMBL files into Bio::Sequence.
* Added functionality to export Bio::Sequence to EMBL format.

Changes:
* renamed Sequence::Format#wrap and #fold to String#wrap and #fold (stored in bio.rb)
* lib/bio/db/common.rb:
    - rewrote def ref and def references
    - added to_biosequence
    - def references now returns an Array instead of a Bio::References object (tests changed accordingly)
* lib/bio/db/embl/embl.rb
    - def ft now returns Array instead of Bio::Features object (tests changed accordingly)
* lib/bio/db/embl/format.erb
* lib/bio/sequence/common.rb
    - added def format_embl


Index: bio.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio.rb,v
retrieving revision 1.89
retrieving revision 1.89.2.1
diff -C2 -d -r1.89 -r1.89.2.1
*** bio.rb	9 Jan 2008 17:18:17 -0000	1.89
--- bio.rb	20 Feb 2008 09:56:22 -0000	1.89.2.1
***************
*** 278,279 ****
--- 278,310 ----
  end
  
+ class String
+   def fold(width = 80)
+     self.gsub(Regexp.new("(.{1,#{width}})"), "\\1\n")
+   end
+   
+   def wrap(width = 80, prefix = '')
+     actual_width = width - prefix.length
+     result = []
+     left = self.dup
+     while left and left.length > actual_width
+       line = nil
+       actual_width.downto(1) do |i|
+         if left[i..i] == ' ' or /[,;]/ =~ left[(i-1)..(i-1)]  then
+           line = left[0..(i-1)].sub(/ +\z/, '')
+           left = left[i..-1].sub(/\A +/, '')
+           break
+         end
+       end
+       if line.nil? then
+         line = left[0..(actual_width-1)]
+         left = left[actual_width..-1]
+       end
+       result << line
+     end
+     result << left if left
+     result_string = result.join("\n#{prefix}")
+     result_string = prefix + result_string unless result_string.empty?
+ #    result_string << "\n" unless result_string.empty?
+     return result_string
+   end
+ end
\ No newline at end of file


From aerts at dev.open-bio.org  Wed Feb 20 04:56:24 2008
From: aerts at dev.open-bio.org (Jan Aerts)
Date: Wed, 20 Feb 2008 09:56:24 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/sequence common.rb, 1.6,
	1.6.2.1 format.rb, 1.4.2.3, 1.4.2.4
Message-ID: <200802200956.m1K9uOhl015806@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/sequence
In directory dev.open-bio.org:/tmp/cvs-serv15755/lib/bio/sequence

Modified Files:
      Tag: BRANCH-biohackathon2008
	common.rb format.rb 
Log Message:
* Rewrote some of the code for converting EMBL files into Bio::Sequence.
* Added functionality to export Bio::Sequence to EMBL format.

Changes:
* renamed Sequence::Format#wrap and #fold to String#wrap and #fold (stored in bio.rb)
* lib/bio/db/common.rb:
    - rewrote def ref and def references
    - added to_biosequence
    - def references now returns an Array instead of a Bio::References object (tests changed accordingly)
* lib/bio/db/embl/embl.rb
    - def ft now returns Array instead of Bio::Features object (tests changed accordingly)
* lib/bio/db/embl/format.erb
* lib/bio/sequence/common.rb
    - added def format_embl


Index: format.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence/format.rb,v
retrieving revision 1.4.2.3
retrieving revision 1.4.2.4
diff -C2 -d -r1.4.2.3 -r1.4.2.4
*** format.rb	15 Feb 2008 02:18:21 -0000	1.4.2.3
--- format.rb	20 Feb 2008 09:56:22 -0000	1.4.2.4
***************
*** 31,106 ****
  #   puts s.output(:embl)
  module Format
- 
-   # INTERNAL USE ONLY, YOU SHOULD NOT CALL THIS METHOD. (And in any
-   # case, it would be difficult to successfully call this method outside
-   # its expected context).
-   #
-   # Output the FASTA format string of the sequence.  
-   #
-   # UNFORTUNATLY, the current implementation of Bio::Sequence is incapable of 
-   # using either the header or width arguments.  So something needs to be
-   # changed...
-   #
-   # Currently, this method is used in Bio::Sequence#output like so,
-   #
-   #   s = Bio::Sequence.new('atgc')
-   #   puts s.output(:fasta)                   #=> "> \natgc\n"
-   # ---
-   # *Arguments*:
-   # * (optional) _header_: String (default nil)
-   # * (optional) _width_: Fixnum (default nil)
-   # *Returns*:: String object
-   def format_fasta(header = nil, width = nil)
-     header ||= "#{@entry_id} #{@definition}"
- 
-     ">#{header}\n" +
-     if width
-       @seq.to_s.gsub(Regexp.new(".{1,#{width}}"), "\\0\n")
-     else
-       @seq.to_s + "\n"
-     end
-   end
- 
-   # Not yet implemented :)
-   # Remove the nodoc command after implementation!
-   # ---
-   # *Returns*:: String object
-   def format_gff #:nodoc:
-     raise NotImplementedError
-   end
- 
-   # INTERNAL USE ONLY, YOU SHOULD NOT CALL THIS METHOD. (And in any
-   # case, it would be difficult to successfully call this method outside
-   # its expected context).
-   #
-   # Output the Genbank format string of the sequence.  
-   # Used in Bio::Sequence#output.
-   # ---
-   # *Returns*:: String object
-   def format_genbank
-     prefix = ' ' * 5
-     indent = prefix + ' ' * 16
-     fwidth = 79 - indent.length
- 
-     format_features(prefix, indent, fwidth)
-   end
- 
-   # INTERNAL USE ONLY, YOU SHOULD NOT CALL THIS METHOD. (And in any
-   # case, it would be difficult to successfully call this method outside
-   # its expected context).
-   #
-   # Output the EMBL format string of the sequence.  
-   # Used in Bio::Sequence#output.
-   # ---
-   # *Returns*:: String object
-   def format_embl
-     prefix = 'FT   '
-     indent = prefix + ' ' * 16
-     fwidth = 80 - indent.length
- 
-     format_features(prefix, indent, fwidth)
-   end
- 
- 
    private
  
--- 31,34 ----
***************
*** 114,123 ****
  
        head = ''
!       wrap(position, width).each_line do |line|
          result << head << line
          head = indent
        end
  
!       result << format_qualifiers(feature.qualifiers, width)
      end
      return result
--- 42,51 ----
  
        head = ''
!       (position).wrap(width).each_line do |line|
          result << head << line
          head = indent
        end
  
!       result << format_qualifiers(feature.qualifiers, indent, width)
      end
      return result
***************
*** 130,136 ****
  
        if v == true
!         lines = wrap('/' + q, width)
        elsif q == 'translation'
!         lines = fold('/' + q + '=' + v, width)
        else
          if v[/\D/]
--- 58,64 ----
  
        if v == true
!         lines =('/' + q).wrap(width)
        elsif q == 'translation'
!         lines = ('/' + q + '="' + v + '"').fold(width)
        else
          if v[/\D/]
***************
*** 139,143 ****
            v = '"' + v + '"'
          end
!         lines = wrap('/' + q + '=' + v, width)
        end
  
--- 67,71 ----
            v = '"' + v + '"'
          end
!         lines = ('/' + q + '=' + v).wrap(width)
        end
  
***************
*** 147,177 ****
    end
  
-   def fold(str, width)
-     str.gsub(Regexp.new("(.{1,#{width}})"), "\\1\n")
-   end
- 
-   def wrap(str, width)
-     result = []
-     left = str.dup
-     while left and left.length > width
-       line = nil
-       width.downto(1) do |i|
-         if left[i..i] == ' ' or /[\,\;]/ =~ left[(i-1)..(i-1)]  then
-           line = left[0..(i-1)].sub(/ +\z/, '')
-           left = left[i..-1].sub(/\A +/, '')
-           break
-         end
-       end
-       if line.nil? then
-         line = left[0..(width-1)]
-         left = left[width..-1]
-       end
-       result << line
-     end
-     result << left if left
-     result_string = result.join("\n")
-     result_string << "\n" unless result_string.empty?
-     return result_string
-   end
  
  end # Format
--- 75,78 ----

Index: common.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence/common.rb,v
retrieving revision 1.6
retrieving revision 1.6.2.1
diff -C2 -d -r1.6 -r1.6.2.1
*** common.rb	27 Dec 2007 17:36:02 -0000	1.6
--- common.rb	20 Feb 2008 09:56:22 -0000	1.6.2.1
***************
*** 38,42 ****
  #   puts dna.randomize
  module Common
! 
    # Return sequence as 
    # String[http://corelib.rubyonrails.org/classes/String.html].
--- 38,42 ----
  #   puts dna.randomize
  module Common
!   
    # Return sequence as 
    # String[http://corelib.rubyonrails.org/classes/String.html].
***************
*** 66,69 ****
--- 66,86 ----
      self.class.new(self)
    end
+   
+   def format_embl
+     output_lines = Array.new
+     counter = 0
+     remainder = self.window_search(60,60) do |subseq|
+       counter += 60
+       subseq.gsub!(/(.{10})/, '\1 ')
+       output_lines.push(' '*5 + subseq + counter.to_s.rjust(9))
+     end
+     counter += remainder.length
+     remainder = (remainder.to_s + ' '*(60-remainder.length))
+     remainder.gsub!(/(.{10})/, '\1 ')
+     output_lines.push(' '*5 + remainder + counter.to_s.rjust(9))
+     return output_lines.join("\n")
+   end
+ 
+ 
  
    # Normalize the current sequence, removing all whitespace and 


From aerts at dev.open-bio.org  Wed Feb 20 04:56:24 2008
From: aerts at dev.open-bio.org (Jan Aerts)
Date: Wed, 20 Feb 2008 09:56:24 +0000
Subject: [BioRuby-cvs] bioruby/test/unit/bio/db/embl test_embl_to_bioseq.rb,
	NONE, 1.1.2.1 test_embl.rb, 1.5, 1.5.2.1 test_embl_rel89.rb,
	1.2, 1.2.2.1
Message-ID: <200802200956.m1K9uOKd015812@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/unit/bio/db/embl
In directory dev.open-bio.org:/tmp/cvs-serv15755/test/unit/bio/db/embl

Modified Files:
      Tag: BRANCH-biohackathon2008
	test_embl.rb test_embl_rel89.rb 
Added Files:
      Tag: BRANCH-biohackathon2008
	test_embl_to_bioseq.rb 
Log Message:
* Rewrote some of the code for converting EMBL files into Bio::Sequence.
* Added functionality to export Bio::Sequence to EMBL format.

Changes:
* renamed Sequence::Format#wrap and #fold to String#wrap and #fold (stored in bio.rb)
* lib/bio/db/common.rb:
    - rewrote def ref and def references
    - added to_biosequence
    - def references now returns an Array instead of a Bio::References object (tests changed accordingly)
* lib/bio/db/embl/embl.rb
    - def ft now returns Array instead of Bio::Features object (tests changed accordingly)
* lib/bio/db/embl/format.erb
* lib/bio/sequence/common.rb
    - added def format_embl


--- NEW FILE: test_embl_to_bioseq.rb ---
#
# test/unit/bio/db/embl/test_embl.rb - Unit test for Bio::EMBL
#
# Copyright::  Copyright (C) 2005, 2008
#                 Mitsuteru Nakao <n at bioruby.org>
#                 Jan Aerts <jan.aerts at bbsrc.ac.uk>
# License::    The Ruby License
#
#  $Id: test_embl_to_bioseq.rb,v 1.1.2.1 2008/02/20 09:56:22 aerts Exp $
#

require 'pathname'
libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
$:.unshift(libpath) unless $:.include?(libpath)

require 'test/unit'
require 'bio'
require 'bio/db/embl/embl'

module Bio
  class TestEMBLToBioSequence < Test::Unit::TestCase
    
    def setup
      bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
      input = File.open(File.join(bioruby_root, 'test', 'data', 'embl', 'AB090716.embl.rel89')).read
      embl_object = Bio::EMBL.new(input)
      embl_object.instance_eval { @data['OS'] = "Haplochromis sp. 'muzu rukwa'" }
      @bio_seq = embl_object.to_biosequence
    end

    def test_entry_id
      assert_equal('AB090716', @bio_seq.entry_id)
    end
    
    def test_primary_accession
      assert_equal('AB090716', @bio_seq.primary_accession)
    end
    
    def test_secondary_accessions
      assert_equal([], @bio_seq.secondary_accessions)
    end
    
    def test_molecule_type
      assert_equal('genomic DNA', @bio_seq.molecule_type)
    end
    
    def test_definition
      assert_equal("Haplochromis sp. 'muzu, rukwa' LWS gene for long wavelength-sensitive opsin, partial cds, specimen_voucher:specimen No. HT-9361.", @bio_seq.definition)
    end

    def test_topology
      assert_equal('linear', @bio_seq.topology)
    end
    
    def test_dates
      assert_equal('25-OCT-2002 (Rel. 73, Created)', @bio_seq.date_created)
      assert_equal('14-NOV-2006 (Rel. 89, Last updated, Version 3)', @bio_seq.date_modified)
    end
    
    def test_division
      assert_equal('VRT', @bio_seq.division)
    end
    
    def test_sequence_version
      assert_equal(1, @bio_seq.sequence_version)
    end
    
    def test_keywords
      assert_equal([], @bio_seq.keywords)
    end
    
    def test_species
      assert_equal("Haplochromis sp. 'muzu, rukwa'", @bio_seq.species)
    end
    
    def test_classification
      assert_equal(['Eukaryota','Metazoa','Chordata','Craniata','Vertebrata','Euteleostomi','Actinopterygii','Neopterygii','Teleostei','Euteleostei','Neoteleostei','Acanthomorpha','Acanthopterygii','Percomorpha','Perciformes','Labroidei','Cichlidae','African cichlids','Pseudocrenilabrinae','Haplochromini','Haplochromis'], @bio_seq.classification)
      

    end

    def test_references
      assert_equal(2, @bio_seq.references.length)
      assert_equal(Bio::Reference, @bio_seq.references[0].class)
    end
    
    def test_features
      assert_equal(3, @bio_seq.features.length)
      assert_equal(Bio::Feature, @bio_seq.features[0].class)
    end
    
  end

  # To really test the Bio::EMBL to Bio::Sequence conversion, we need to test if
  # that Bio::Sequence can be made into a valid Bio::EMBL again.
  class TestEMBLToBioSequenceRoundTrip < Test::Unit::TestCase
    def setup
      bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
      input = File.open(File.join(bioruby_root, 'test', 'data', 'embl', 'AB090716.embl.rel89')).read
      embl_object_1 = Bio::EMBL.new(input)
      embl_object_1.instance_eval { @data['OS'] = "Haplochromis sp. 'muzu rukwa'" }
      @bio_seq_1 = embl_object_1.to_biosequence
      embl_object_2 = Bio::EMBL.new(@bio_seq_1.output(:embl))
      @bio_seq_2 = embl_object_2.to_biosequence
    end
    
    def test_entry_id
      assert_equal('AB090716', @bio_seq_2.entry_id)
    end
    
    def test_primary_accession
      assert_equal('AB090716', @bio_seq_2.primary_accession)
    end
    
    def test_secondary_accessions
      assert_equal([], @bio_seq_2.secondary_accessions)
    end
    
    def test_molecule_type
      assert_equal('genomic DNA', @bio_seq_2.molecule_type)
    end
    
    def test_definition
      assert_equal("Haplochromis sp. 'muzu, rukwa' LWS gene for long wavelength-sensitive opsin, partial cds, specimen_voucher:specimen No. HT-9361.", @bio_seq_2.definition)
    end

    def test_topology
      assert_equal('linear', @bio_seq_2.topology)
    end
    
    def test_dates
      assert_equal('25-OCT-2002 (Rel. 73, Created)', @bio_seq_2.date_created)
      assert_equal('14-NOV-2006 (Rel. 89, Last updated, Version 3)', @bio_seq_2.date_modified)
    end
    
    def test_division
      assert_equal('VRT', @bio_seq_2.division)
    end
    
    def test_sequence_version
      assert_equal(1, @bio_seq_2.sequence_version)
    end
    
    def test_keywords
      assert_equal([], @bio_seq_2.keywords)
    end
    
    def test_species
      assert_equal("Haplochromis sp. 'muzu, rukwa'", @bio_seq_2.species)
    end
    
    def test_classification
      assert_equal(['Eukaryota','Metazoa','Chordata','Craniata','Vertebrata','Euteleostomi','Actinopterygii','Neopterygii','Teleostei','Euteleostei','Neoteleostei','Acanthomorpha','Acanthopterygii','Percomorpha','Perciformes','Labroidei','Cichlidae','African cichlids','Pseudocrenilabrinae','Haplochromini','Haplochromis'], @bio_seq_2.classification)
      

    end

    def test_references
      assert_equal(2, @bio_seq_2.references.length)
      assert_equal(Bio::Reference, @bio_seq_2.references[0].class)
    end
    
    def test_features a
      assert_equal(3, @bio_seq_2.features.length)
      assert_equal(Bio::Feature, @bio_seq_2.features[0].class)
    end
  end
end


Index: test_embl_rel89.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/embl/test_embl_rel89.rb,v
retrieving revision 1.2
retrieving revision 1.2.2.1
diff -C2 -d -r1.2 -r1.2.2.1
*** test_embl_rel89.rb	5 Apr 2007 23:35:43 -0000	1.2
--- test_embl_rel89.rb	20 Feb 2008 09:56:22 -0000	1.2.2.1
***************
*** 156,160 ****
      # Bio::EMBLDB::COMMON#references
      def test_references 
!       assert_equal(Bio::References, @obj.references.class)
      end
  
--- 156,160 ----
      # Bio::EMBLDB::COMMON#references
      def test_references 
!       assert_equal(Array, @obj.references.class)
      end
  
***************
*** 169,173 ****
  
      def test_ft
!       assert_equal(Bio::Features, @obj.ft.class)
      end
  
--- 169,173 ----
  
      def test_ft
!       assert_equal(Array, @obj.ft.class)
      end
  
***************
*** 179,183 ****
  
      def test_ft_accessor
!       assert_equal('CDS', @obj.ft.features[1].feature)
      end
  
--- 179,183 ----
  
      def test_ft_accessor
!       assert_equal('CDS', @obj.ft[1].feature)
      end
  

Index: test_embl.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/embl/test_embl.rb,v
retrieving revision 1.5
retrieving revision 1.5.2.1
diff -C2 -d -r1.5 -r1.5.2.1
*** test_embl.rb	5 Apr 2007 23:35:43 -0000	1.5
--- test_embl.rb	20 Feb 2008 09:56:22 -0000	1.5.2.1
***************
*** 151,155 ****
      # Bio::EMBLDB::COMMON#references
      def test_references 
!       assert_equal(Bio::References, @obj.references.class)
      end
  
--- 151,155 ----
      # Bio::EMBLDB::COMMON#references
      def test_references 
!       assert_equal(Array, @obj.references.class)
      end
  
***************
*** 164,168 ****
  
      def test_ft
!       assert_equal(Bio::Features, @obj.ft.class)
      end
  
--- 164,168 ----
  
      def test_ft
!       assert_equal(Array, @obj.ft.class)
      end
  
***************
*** 174,178 ****
  
      def test_ft_accessor
!       assert_equal('CDS', @obj.ft.features[1].feature)
      end
  
--- 174,178 ----
  
      def test_ft_accessor
!       assert_equal('CDS', @obj.ft[1].feature)
      end
  


From aerts at dev.open-bio.org  Wed Feb 20 08:54:21 2008
From: aerts at dev.open-bio.org (Jan Aerts)
Date: Wed, 20 Feb 2008 13:54:21 +0000
Subject: [BioRuby-cvs] bioruby/lib bio.rb,1.89.2.1,1.89.2.2
Message-ID: <200802201354.m1KDsL5F016175@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib
In directory dev.open-bio.org:/tmp/cvs-serv16153

Modified Files:
      Tag: BRANCH-biohackathon2008
	bio.rb 
Log Message:
Fixed bug in formatting features when exporting to EMBL.


Index: bio.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio.rb,v
retrieving revision 1.89.2.1
retrieving revision 1.89.2.2
diff -C2 -d -r1.89.2.1 -r1.89.2.2
*** bio.rb	20 Feb 2008 09:56:22 -0000	1.89.2.1
--- bio.rb	20 Feb 2008 13:54:19 -0000	1.89.2.2
***************
*** 280,284 ****
  class String
    def fold(width = 80)
!     self.gsub(Regexp.new("(.{1,#{width}})"), "\\1\n")
    end
    
--- 280,284 ----
  class String
    def fold(width = 80)
!     self.gsub(Regexp.new("(.{1,#{width}})"), "\\1\n").sub(/\n$/, '')
    end
    
***************
*** 308,310 ****
      return result_string
    end
! end
\ No newline at end of file
--- 308,310 ----
      return result_string
    end
! end


From aerts at dev.open-bio.org  Wed Feb 20 08:54:21 2008
From: aerts at dev.open-bio.org (Jan Aerts)
Date: Wed, 20 Feb 2008 13:54:21 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/sequence format.rb,1.4.2.4,1.4.2.5
Message-ID: <200802201354.m1KDsLWx016180@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/sequence
In directory dev.open-bio.org:/tmp/cvs-serv16153/bio/sequence

Modified Files:
      Tag: BRANCH-biohackathon2008
	format.rb 
Log Message:
Fixed bug in formatting features when exporting to EMBL.


Index: format.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence/format.rb,v
retrieving revision 1.4.2.4
retrieving revision 1.4.2.5
diff -C2 -d -r1.4.2.4 -r1.4.2.5
*** format.rb	20 Feb 2008 09:56:22 -0000	1.4.2.4
--- format.rb	20 Feb 2008 13:54:19 -0000	1.4.2.5
***************
*** 47,51 ****
--- 47,53 ----
        end
  
+       result << "\n"
        result << format_qualifiers(feature.qualifiers, indent, width)
+       result << "\n"
      end
      return result
***************
*** 62,66 ****
          lines = ('/' + q + '="' + v + '"').fold(width)
        else
!         if v[/\D/]
            #v.delete!("\x00-\x1f\x7f-\xff")
            v.gsub!(/"/, '""')
--- 64,68 ----
          lines = ('/' + q + '="' + v + '"').fold(width)
        else
!         if ( v[/\D/] or q == 'chromosome' )
            #v.delete!("\x00-\x1f\x7f-\xff")
            v.gsub!(/"/, '""')
***************
*** 72,76 ****
        lines.gsub!(/^/, indent)
        lines
!     end.join
    end
  
--- 74,78 ----
        lines.gsub!(/^/, indent)
        lines
!     end.join("\n")
    end
  


From ngoto at dev.open-bio.org  Wed Feb 20 12:04:49 2008
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Wed, 20 Feb 2008 17:04:49 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio reference.rb,1.24.2.1,1.24.2.2
Message-ID: <200802201704.m1KH4nCF017912@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv17810/lib/bio

Modified Files:
      Tag: BRANCH-biohackathon2008
	reference.rb 
Log Message:
Bio::References#new is added not to create Bio::References instances anymore.
New transitional module Bio::References::BackwardCompatibilityForBioReferences 
is added to help keeping backward compatibility.
(The only reason why not to erase Bio::References class is to load
Marshal.dump data.)


Index: reference.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/reference.rb,v
retrieving revision 1.24.2.1
retrieving revision 1.24.2.2
diff -C2 -d -r1.24.2.1 -r1.24.2.2
*** reference.rb	18 Feb 2008 15:44:39 -0000	1.24.2.1
--- reference.rb	20 Feb 2008 17:04:47 -0000	1.24.2.2
***************
*** 580,587 ****
--- 580,593 ----
    # = DESCRIPTION
    #
+   # This class is OBSOLETED, and will soon be removed.
+   # Instead of this class, an array is to be used.
+   #
+   # 
    # A container class for Bio::Reference objects.
    #
    # = USAGE
    #
+   # This class should NOT be used.
+   #
    #   refs = Bio::References.new
    #   refs.append(Bio::Reference.new(hash))
***************
*** 591,596 ****
    #
    class References
!     include Enumerable
!     
      # Array of Bio::Reference objects
      attr_accessor :references
--- 597,638 ----
    #
    class References
! 
!     # module to keep backward compatibility with obsoleted Bio::References
!     module BackwardCompatibilityForBioReferences #:nodoc:
! 
!       # Backward compatibility with Bio::References#references.
!       # Now, references are stored in an array, and
!       # you should change your code not to use this method.
!       def references
!         warn 'Bio::References is obsoleted. Now, references are stored in an array.'
!         self
!       end
! 
!       # Backward compatibility with Bio::References#append.
!       # Now, references are stored in an array, and
!       # you should change your code not to use this method.
!       def append(reference)
!         warn 'Bio::References is obsoleted. Now, references are stored in an array.'
!         self.push(reference) if reference.is_a? Reference
!         self
!       end
!     end #module BackwardCompatibilityForBioReferences
! 
!     # This method should not be used.
!     # Only for backward compatibility of existing code.
!     #
!     # Since Bio::References is obsoleted,
!     # Bio::References.new not returns Bio::References object,
!     # but modifies given _ary_ and returns the _ary_.
!     #
!     # *Arguments*:
!     # * (optional) __: Array of Bio::Reference objects
!     # *Returns*:: the given array
!     def self.new(ary = [])
!       warn 'Bio::References is obsoleted. Some methods are added to given array to keep backward compatibility.'
!       ary.extend(BackwardCompatibilityForBioReferences)
!       ary
!     end
! 
      # Array of Bio::Reference objects
      attr_accessor :references


From ngoto at dev.open-bio.org  Fri Feb 22 09:26:18 2008
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Fri, 22 Feb 2008 14:26:18 +0000
Subject: [BioRuby-cvs] bioruby/lib bio.rb,1.89.2.2,1.89.2.3
Message-ID: <200802221426.m1MEQI5W030582@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib
In directory dev.open-bio.org:/tmp/cvs-serv30562

Modified Files:
      Tag: BRANCH-biohackathon2008
	bio.rb 
Log Message:
reverted to 1.89


Index: bio.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio.rb,v
retrieving revision 1.89.2.2
retrieving revision 1.89.2.3
diff -C2 -d -r1.89.2.2 -r1.89.2.3
*** bio.rb	20 Feb 2008 13:54:19 -0000	1.89.2.2
--- bio.rb	22 Feb 2008 14:26:16 -0000	1.89.2.3
***************
*** 278,310 ****
  end
  
- class String
-   def fold(width = 80)
-     self.gsub(Regexp.new("(.{1,#{width}})"), "\\1\n").sub(/\n$/, '')
-   end
-   
-   def wrap(width = 80, prefix = '')
-     actual_width = width - prefix.length
-     result = []
-     left = self.dup
-     while left and left.length > actual_width
-       line = nil
-       actual_width.downto(1) do |i|
-         if left[i..i] == ' ' or /[,;]/ =~ left[(i-1)..(i-1)]  then
-           line = left[0..(i-1)].sub(/ +\z/, '')
-           left = left[i..-1].sub(/\A +/, '')
-           break
-         end
-       end
-       if line.nil? then
-         line = left[0..(actual_width-1)]
-         left = left[actual_width..-1]
-       end
-       result << line
-     end
-     result << left if left
-     result_string = result.join("\n#{prefix}")
-     result_string = prefix + result_string unless result_string.empty?
- #    result_string << "\n" unless result_string.empty?
-     return result_string
-   end
- end
--- 278,279 ----


From ngoto at dev.open-bio.org  Fri Feb 22 09:30:46 2008
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Fri, 22 Feb 2008 14:30:46 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/sequence format.rb,1.4.2.5,1.4.2.6
Message-ID: <200802221430.m1MEUknT030652@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/sequence
In directory dev.open-bio.org:/tmp/cvs-serv30611

Modified Files:
      Tag: BRANCH-biohackathon2008
	format.rb 
Log Message:
 * fold() and wrap() are reverted
 * Bug fix in format_features() and format_qualifiers()
 * The content of 'translate' qualifier is now wrapped by double quote


Index: format.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence/format.rb,v
retrieving revision 1.4.2.5
retrieving revision 1.4.2.6
diff -C2 -d -r1.4.2.5 -r1.4.2.6
*** format.rb	20 Feb 2008 13:54:19 -0000	1.4.2.5
--- format.rb	22 Feb 2008 14:30:44 -0000	1.4.2.6
***************
*** 31,34 ****
--- 31,109 ----
  #   puts s.output(:embl)
  module Format
+ 
+   # INTERNAL USE ONLY, YOU SHOULD NOT CALL THIS METHOD. (And in any
+   # case, it would be difficult to successfully call this method outside
+   # its expected context).
+   #
+   # Output the FASTA format string of the sequence.  
+   #
+   # UNFORTUNATLY, the current implementation of Bio::Sequence is incapable of 
+   # using either the header or width arguments.  So something needs to be
+   # changed...
+   #
+   # Currently, this method is used in Bio::Sequence#output like so,
+   #
+   #   s = Bio::Sequence.new('atgc')
+   #   puts s.output(:fasta)                   #=> "> \natgc\n"
+   # ---
+   # *Arguments*:
+   # * (optional) _header_: String (default nil)
+   # * (optional) _width_: Fixnum (default nil)
+   # *Returns*:: String object
+   def format_fasta(header = nil, width = nil)
+     header ||= "#{@entry_id} #{@definition}"
+ 
+     ">#{header}\n" +
+     if width
+       @seq.to_s.gsub(Regexp.new(".{1,#{width}}"), "\\0\n")
+     else
+       @seq.to_s + "\n"
+     end
+   end
+ 
+   #---
+ 
+   # Not yet implemented :)
+   # Remove the nodoc command after implementation!
+   # ---
+   # *Returns*:: String object
+   #def format_gff #:nodoc:
+   #  raise NotImplementedError
+   #end
+ 
+   # INTERNAL USE ONLY, YOU SHOULD NOT CALL THIS METHOD. (And in any
+   # case, it would be difficult to successfully call this method outside
+   # its expected context).
+   #
+   # Output the Genbank format string of the sequence.  
+   # Used in Bio::Sequence#output.
+   # ---
+   # *Returns*:: String object
+   #def format_genbank
+   #  prefix = ' ' * 5
+   #  indent = prefix + ' ' * 16
+   #  fwidth = 79 - indent.length
+   #
+   #  format_features(prefix, indent, fwidth)
+   #end
+ 
+   # INTERNAL USE ONLY, YOU SHOULD NOT CALL THIS METHOD. (And in any
+   # case, it would be difficult to successfully call this method outside
+   # its expected context).
+   #
+   # Output the EMBL format string of the sequence.  
+   # Used in Bio::Sequence#output.
+   # ---
+   # *Returns*:: String object
+   #def format_embl
+   #  prefix = 'FT   '
+   #  indent = prefix + ' ' * 16
+   #  fwidth = 80 - indent.length
+   #
+   #  format_features(prefix, indent, fwidth)
+   #end
+ 
+   #+++
+ 
    private
  
***************
*** 42,53 ****
  
        head = ''
!       (position).wrap(width).each_line do |line|
          result << head << line
          head = indent
        end
  
-       result << "\n"
        result << format_qualifiers(feature.qualifiers, indent, width)
-       result << "\n"
      end
      return result
--- 117,126 ----
  
        head = ''
!       wrap(position, width).each_line do |line|
          result << head << line
          head = indent
        end
  
        result << format_qualifiers(feature.qualifiers, indent, width)
      end
      return result
***************
*** 60,80 ****
  
        if v == true
!         lines =('/' + q).wrap(width)
        elsif q == 'translation'
!         lines = ('/' + q + '="' + v + '"').fold(width)
        else
!         if ( v[/\D/] or q == 'chromosome' )
            #v.delete!("\x00-\x1f\x7f-\xff")
            v.gsub!(/"/, '""')
            v = '"' + v + '"'
          end
!         lines = ('/' + q + '=' + v).wrap(width)
        end
  
        lines.gsub!(/^/, indent)
        lines
!     end.join("\n")
    end
  
  
  end # Format
--- 133,180 ----
  
        if v == true
!         lines = wrap('/' + q, width)
        elsif q == 'translation'
!         lines = fold("/#{q}=\"#{v}\"", width)
        else
!         if v[/\D/] or q == 'chromosome'
            #v.delete!("\x00-\x1f\x7f-\xff")
            v.gsub!(/"/, '""')
            v = '"' + v + '"'
          end
!         lines = wrap('/' + q + '=' + v, width)
        end
  
        lines.gsub!(/^/, indent)
        lines
!     end.join
!   end
! 
!   def fold(str, width)
!     str.gsub(Regexp.new("(.{1,#{width}})"), "\\1\n")
    end
  
+   def wrap(str, width)
+     result = []
+     left = str.dup
+     while left and left.length > width
+       line = nil
+       width.downto(1) do |i|
+         if left[i..i] == ' ' or /[\,\;]/ =~ left[(i-1)..(i-1)]  then
+           line = left[0..(i-1)].sub(/ +\z/, '')
+           left = left[i..-1].sub(/\A +/, '')
+           break
+         end
+       end
+       if line.nil? then
+         line = left[0..(width-1)]
+         left = left[width..-1]
+       end
+       result << line
+     end
+     result << left if left
+     result_string = result.join("\n")
+     result_string << "\n" unless result_string.empty?
+     return result_string
+   end
  
  end # Format


From ngoto at dev.open-bio.org  Thu Feb 28 00:51:05 2008
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Thu, 28 Feb 2008 05:51:05 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio reference.rb,1.24.2.2,1.24.2.3
Message-ID: <200802280551.m1S5p5eX020471@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv20451

Modified Files:
      Tag: BRANCH-biohackathon2008
	reference.rb 
Log Message:
@sequence_position should be nil if no information available


Index: reference.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/reference.rb,v
retrieving revision 1.24.2.2
retrieving revision 1.24.2.3
diff -C2 -d -r1.24.2.2 -r1.24.2.3
*** reference.rb	20 Feb 2008 17:04:47 -0000	1.24.2.2
--- reference.rb	28 Feb 2008 05:51:03 -0000	1.24.2.3
***************
*** 138,142 ****
        @mesh     = hash['mesh']
        @embl_gb_record_number = hash['embl_gb_record_number'] || nil
!       @sequence_position = hash['sequence_position'] || []
        @comments = hash['comments'] || []
        @xrefs    = hash['xrefs'] || []
--- 138,142 ----
        @mesh     = hash['mesh']
        @embl_gb_record_number = hash['embl_gb_record_number'] || nil
!       @sequence_position = hash['sequence_position'] || nil
        @comments = hash['comments'] || []
        @xrefs    = hash['xrefs'] || []
***************
*** 280,284 ****
          end
        end
!       if @sequence_position != ''
          lines << "RP   #{@sequence_position}"
        end
--- 280,284 ----
          end
        end
!       if ! @sequence_position.nil?
          lines << "RP   #{@sequence_position}"
        end


From ngoto at dev.open-bio.org  Thu Feb 28 00:54:53 2008
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Thu, 28 Feb 2008 05:54:53 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/db/genbank common.rb,1.11,1.11.2.1
Message-ID: <200802280554.m1S5sr5Z020520@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/db/genbank
In directory dev.open-bio.org:/tmp/cvs-serv20500/db/genbank

Modified Files:
      Tag: BRANCH-biohackathon2008
	common.rb 
Log Message:
changed to parse sequence position and reference number in REFERENCES


Index: common.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/genbank/common.rb,v
retrieving revision 1.11
retrieving revision 1.11.2.1
diff -C2 -d -r1.11 -r1.11.2.1
*** common.rb	5 Apr 2007 23:35:40 -0000	1.11
--- common.rb	28 Feb 2008 05:54:51 -0000	1.11.2.1
***************
*** 141,144 ****
--- 141,149 ----
          subtag2array(ref).each do |field|
            case tag_get(field)
+           when /^\s*REFERENCE\s+(\d+)(\s+\(bases\s+(\d+)\s+to\s+(\d+)\))?/
+             hash['embl_gb_record_number'] = $1.to_i
+             if $2 then
+               hash['sequence_position'] = "#{$3}-#{$4}"
+             end
            when /AUTHORS/
              authors = truncate(tag_cut(field))


From pjotr at dev.open-bio.org  Sat Feb  2 08:03:36 2008
From: pjotr at dev.open-bio.org (Pjotr Prins)
Date: Sat, 02 Feb 2008 13:03:36 -0000
Subject: [BioRuby-cvs] bioruby/doc Tutorial.rd,1.13,1.14
Message-ID: <200802021303.m12D3PNX031194@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/doc
In directory dev.open-bio.org:/tmp/cvs-serv31174

Modified Files:
	Tutorial.rd 
Log Message:
Tabs in the Tutorial broke the rd parser - the Wiki will be fixed now.



Index: Tutorial.rd
===================================================================
RCS file: /home/repository/bioruby/bioruby/doc/Tutorial.rd,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** Tutorial.rd	9 Jul 2007 12:28:07 -0000	1.13
--- Tutorial.rd	2 Feb 2008 13:03:23 -0000	1.14
***************
*** 1,2 ****
--- 1,10 ----
+ # This document is generated with a version of rd2html (part of Hiki)
+ #
+ # A possible test run could be from rdtool:
+ #
+ #   ruby -I lib ./bin/rd2 ~/izip/cvs/opensource/bioruby/doc/Tutorial.rd
+ #
+ # A common problem is tabs in the text file!
+ 
  =begin
  
***************
*** 5,13 ****
    $Id$
  
! Translated into English: Naohisa Goto <ng at bioruby.org>
  
! Editor:                  PjotrPrins <p at bioruby.org>
  
! Copyright (C) 2001-2003 KATAYAMA Toshiaki <k at bioruby.org>, 2005-2007 Pjotr Prins, Naohisa Goto and others
  
  IMPORTANT NOTICE: This page is maintained in the BioRuby CVS
--- 13,21 ----
    $Id$
  
! Translated into English: Naohisa Goto <ng .at. bioruby.org>
  
! Editor:                  PjotrPrins <p .at. bioruby.org>
  
! Copyright (C) 2001-2003 KATAYAMA Toshiaki <k .at. bioruby.org>, 2005-2008 Pjotr Prins, Naohisa Goto and others
  
  IMPORTANT NOTICE: This page is maintained in the BioRuby CVS
***************
*** 32,36 ****
  version it has with the
  
! 	% ruby -v
  
  command. Showing something like:
--- 40,44 ----
  version it has with the
  
!   % ruby -v
  
  command. Showing something like:
***************
*** 55,59 ****
    bioruby> puts seq
    atgcatgcaaaa
!   bioruby> puts seq.complement 
    ttttgcatgcat
  
--- 63,67 ----
    bioruby> puts seq
    atgcatgcaaaa
!   bioruby> puts seq.complement
    ttttgcatgcat
  
***************
*** 94,98 ****
      puts seq.complement.translate       # translation of complemental strand
  
! 		counts = {'a'=>seq.count('a'),'c'=>seq.count('c'),'g'=>seq.count('g'),'t'=>seq.count('t')}
      p randomseq = Bio::Sequence::NA.randomize(counts)  # reshuffle sequence with same freq.
  
--- 102,106 ----
      puts seq.complement.translate       # translation of complemental strand
  
!     counts = {'a'=>seq.count('a'),'c'=>seq.count('c'),'g'=>seq.count('g'),'t'=>seq.count('t')}
      p randomseq = Bio::Sequence::NA.randomize(counts)  # reshuffle sequence with same freq.
  
***************
*** 159,163 ****
  * Divide a genome sequence into sections of 10000bp and
    output FASTA formatted sequences. The 1000bp at the start and end of
! 	each subsequence overlapped. At the 3' end of the sequence the
    leftover subsequence shorter than 10000bp is also added
  
--- 167,171 ----
  * Divide a genome sequence into sections of 10000bp and
    output FASTA formatted sequences. The 1000bp at the start and end of
!   each subsequence overlapped. At the 3' end of the sequence the
    leftover subsequence shorter than 10000bp is also added
  
***************
*** 252,258 ****
  
      #!/usr/bin/env ruby
!   
      require 'bio'
!     
      ff = Bio::FlatFile.new(Bio::GenBank, ARGF)
      ff.each_entry do |gb|
--- 260,266 ----
  
      #!/usr/bin/env ruby
! 
      require 'bio'
! 
      ff = Bio::FlatFile.new(Bio::GenBank, ARGF)
      ff.each_entry do |gb|
***************
*** 470,475 ****
  
    rebase = Bio::RestrictionEnzyme.rebase
! 	rebase.each do |enzyme_name, info|
! 		p enzyme_name
    end
  
--- 478,483 ----
  
    rebase = Bio::RestrictionEnzyme.rebase
!   rebase.each do |enzyme_name, info|
!     p enzyme_name
    end
  
***************
*** 483,488 ****
        end
     end
! 	 res.each do |frag|
! 	    em = EnzymeMatch.new
  
        em.p_left = frag.p_left
--- 491,496 ----
        end
     end
!    res.each do |frag|
!       em = EnzymeMatch.new
  
        em.p_left = frag.p_left
***************
*** 494,498 ****
        em.enzyme = ar_enz
        em.sequence = ar_seq
! 			p em
      end
  
--- 502,506 ----
        em.enzyme = ar_enz
        em.sequence = ar_seq
!       p em
      end
  
***************
*** 1160,1168 ****
  == Comparing BioProjects
  
! For a quick functional comparison of BioRuby, BioPerl, BioPython and Bioconductor (R) see ((<http://sciruby.codeforpeople.com/sr.cgi/BioProjects>))
  
  == Using BioRuby with R
  
! Using Ruby with R Pjotr wrote a section on SciRuby. See ((<ULR:http://sciruby.codeforpeople.com/sr.cgi/RubyWithRlang>))
  
  == Using BioPerl or BioPython from Ruby
--- 1168,1176 ----
  == Comparing BioProjects
  
! For a quick functional comparison of BioRuby, BioPerl, BioPython and Bioconductor (R) see ((<URL:http://sciruby.codeforpeople.com/sr.cgi/BioProjects>))
  
  == Using BioRuby with R
  
! Using Ruby with R Pjotr wrote a section on SciRuby. See ((<URL:http://sciruby.codeforpeople.com/sr.cgi/RubyWithRlang>))
  
  == Using BioPerl or BioPython from Ruby
***************
*** 1182,1184 ****
  
  =end
- 
--- 1190,1191 ----


From pjotr at dev.open-bio.org  Sat Feb  2 09:02:03 2008
From: pjotr at dev.open-bio.org (Pjotr Prins)
Date: Sat, 02 Feb 2008 14:02:03 -0000
Subject: [BioRuby-cvs] bioruby/doc Tutorial.rd,1.14,1.15
Message-ID: <200802021401.m12E1uuN031293@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/doc
In directory dev.open-bio.org:/tmp/cvs-serv31273

Modified Files:
	Tutorial.rd 
Log Message:
Updating tutorial

Index: Tutorial.rd
===================================================================
RCS file: /home/repository/bioruby/bioruby/doc/Tutorial.rd,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** Tutorial.rd	2 Feb 2008 13:03:23 -0000	1.14
--- Tutorial.rd	2 Feb 2008 14:01:54 -0000	1.15
***************
*** 3,7 ****
  # A possible test run could be from rdtool:
  #
! #   ruby -I lib ./bin/rd2 ~/izip/cvs/opensource/bioruby/doc/Tutorial.rd
  #
  # A common problem is tabs in the text file!
--- 3,12 ----
  # A possible test run could be from rdtool:
  #
! #   ruby -I lib ./bin/rd2 ~/cvs/opensource/bioruby/doc/Tutorial.rd
! #
! # or with style sheet:
! #
! #   ruby -I lib ./bin/rd2 -r rd/rd2html-lib.rb --with-c
! ss=bioruby.css ~/cvs/opensource/bioruby/doc/Tutorial.rd > ~/bioruby.html
  #
  # A common problem is tabs in the text file!
***************
*** 9,39 ****
  =begin
  
! See the document in the CVS repository ./doc/((<Tutorial.rd|URL:http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/*checkout*/bioruby/doc/Tutorial.rd?rev=HEAD&cvsroot=bioruby&content-type=text/plain>)) - for a potentially more up-to-date edition. This one was updated:
! 
!   $Id$
  
! Translated into English: Naohisa Goto <ng .at. bioruby.org>
  
! Editor:                  PjotrPrins <p .at. bioruby.org>
  
! Copyright (C) 2001-2003 KATAYAMA Toshiaki <k .at. bioruby.org>, 2005-2008 Pjotr Prins, Naohisa Goto and others
  
! IMPORTANT NOTICE: This page is maintained in the BioRuby CVS
! repository. Please edit the file there otherwise changes may get
! lost. See ((<BioRuby Developer Information>)) for CVS and mailing list
! access.
  
! = BioRuby Tutorial
  
  == Introduction
  
! This is a tutorial for using Bioruby. For BioRuby you need to install
! Ruby and the BioRuby package on your computer. For each following the
! instruction on the respective websites. (EDITOR's NOTE: include URL's)
! 
! (EDITOR's NOTE: describe rdoc use for individual classes)
  
! For further information on the Ruby language see the section 'Further
! reading' at the end.
  
  You can check whether Ruby is installed on your computer and what
--- 14,40 ----
  =begin
  
! = BioRuby Tutorial
  
! Editor: PjotrPrins <p .at. bioruby.org>
  
! * Copyright (C) 2001-2003 KATAYAMA Toshiaki <k .at. bioruby.org>
! * Copyright (C) 2005-2008 Pjotr Prins, Naohisa Goto and others
  
! The latest version resides in the CVS repository ./doc/((<Tutorial.rd|URL:http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/*checkout*/bioruby/doc/Tutorial.rd?rev=HEAD&cvsroot=bioruby&content-type=text/plain>)). This one was updated:
  
!   $Id$ 
  
! in preparation for the ((<BioHackathlon 2008|URL:http://hackathon.dbcls.jp/>))
  
  == Introduction
  
! This is a tutorial for using Bioruby. A basic knowledge of Ruby is required.
! If you want to know more about the programming langauge Ruby we recommend the
! excellent book ((<Programming Ruby|URL:http://www.pragprog.com/titles/ruby>))
! by Dave Thomas and Andy Hunt - some of it is online
! ((<here|URL:http://www.rubycentral.com/pickaxe/>)).
  
! For BioRuby you need to install
! Ruby and the BioRuby package on your computer.
  
  You can check whether Ruby is installed on your computer and what
***************
*** 46,49 ****
--- 47,61 ----
    ruby 1.8.5 (2006-08-25) [powerpc-linux]
  
+ If you see no such thing you'll have to install Ruby using your installation
+ manager. For more information see the
+ ((<Ruby|URL:http://www.ruby-lang.org/en/>)) website.
+ 
+ Once Ruby is works download and install Bioruby using the links on the
+ ((<Bioruby|URL:http://bioruby.org/>)) website.
+ 
+ A lot of BioRuby's documentation exists in the source code and unit tests. To
+ really dive in you will need the latest source code tree. The embedded rdoc
+ documentation can be viewed online at
+ ((<bioruby's rdoc|URL:http://bioruby.org/rdoc/>)). But first lets start!
  
  == Trying Bioruby
***************
*** 52,56 ****
  following command
  
!   $BIORUBY/bin/bioruby
  
  and you should see a prompt
--- 64,68 ----
  following command
  
!   ./bin/bioruby
  
  and you should see a prompt
***************
*** 93,97 ****
      puts seq.translate                  # translation (Bio::Sequence::AA object)
      puts seq.translate(2)               # translation from frame 2 (default is frame 1)
!     puts seq.translate(1,11)            # using codon table No.11 (see http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi)
  
      p seq.translate.codes               # shows three-letter codes (Array)
--- 105,110 ----
      puts seq.translate                  # translation (Bio::Sequence::AA object)
      puts seq.translate(2)               # translation from frame 2 (default is frame 1)
!     puts seq.translate(1,11)            # using codon table No.11 
!                                         # (see http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi)
  
      p seq.translate.codes               # shows three-letter codes (Array)
***************
*** 114,120 ****
    % ri File.open
  
! Nucleic acid sequence is an object of +Bio::Sequence::NA+ class, and
! amino acid sequence is an object of +Bio::Sequence::AA+ class.  Shared
! methods are in the parent +Bio::Sequence+ class.
  
  As Bio::Sequence class inherits Ruby's String class, you can use
--- 127,133 ----
    % ri File.open
  
! Nucleic acid sequence is an object of Bio::Sequence::NA class, and
! amino acid sequence is an object of Bio::Sequence::AA class.  Shared
! methods are in the parent Bio::Sequence class.
  
  As Bio::Sequence class inherits Ruby's String class, you can use
***************
*** 297,303 ****
      end
  
- (TRANSLATOR'S NOTE: Bio::DB.open have not been used so well.)
- (EDITOR's NOTE: Test code)
- 
  Next, we are going to parse the GenBank 'features', which is normally
  very complicated:
--- 310,313 ----
***************
*** 382,387 ****
  
  Databases in BioRuby are essentially accessed like that of GenBank
! with classes like Bio::GenBank, Bio::KEGG::GENES,
! (EDITOR's NOTE: include complete list)
  
  In many cases the Bio::DatabaseClass acts as a factory pattern
--- 392,397 ----
  
  Databases in BioRuby are essentially accessed like that of GenBank
! with classes like Bio::GenBank, Bio::KEGG::GENES. A full list can be found in 
! the ./lib/bio/db directory of the BioRuby source tree.
  
  In many cases the Bio::DatabaseClass acts as a factory pattern
***************
*** 1151,1160 ****
  == Further reading
  
! See the BioRuby in anger Wiki and the class documentation for more
! information on BioRuby.
  
- The best book to get for understanding and getting productive with the
- Ruby language is 'Programming Ruby' by Dave Thomas and Andy
- Hunt. Strongly recommended!
  
  = APPENDIX
--- 1161,1169 ----
  == Further reading
  
! See the BioRuby in anger Wiki.  A lot of BioRuby's documentation exists in the
! source code and unit tests. To really dive in you will need the latest source
! code tree. The embedded rdoc documentation can be viewed online at
! ((<URL:http://bioruby.org/rdoc/>)).
  
  
  = APPENDIX
***************
*** 1189,1191 ****
--- 1198,1207 ----
  carefully that come with each package.
  
+ == Modifying this page
+ 
+ IMPORTANT NOTICE: This page is maintained in the BioRuby CVS
+ repository. Please edit the file there otherwise changes may get
+ lost. See ((<BioRuby Developer Information>)) for CVS and mailing list
+ access.
+ 
  =end


From pjotr at dev.open-bio.org  Sat Feb  2 09:15:19 2008
From: pjotr at dev.open-bio.org (Pjotr Prins)
Date: Sat, 02 Feb 2008 14:15:19 -0000
Subject: [BioRuby-cvs] bioruby/doc Tutorial.rd,1.15,1.16
Message-ID: <200802021415.m12EFAqB031346@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/doc
In directory dev.open-bio.org:/tmp/cvs-serv31326

Modified Files:
	Tutorial.rd 
Log Message:
Modified tutorial

Index: Tutorial.rd
===================================================================
RCS file: /home/repository/bioruby/bioruby/doc/Tutorial.rd,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** Tutorial.rd	2 Feb 2008 14:01:54 -0000	1.15
--- Tutorial.rd	2 Feb 2008 14:15:08 -0000	1.16
***************
*** 115,120 ****
      puts seq.complement.translate       # translation of complemental strand
  
!     counts = {'a'=>seq.count('a'),'c'=>seq.count('c'),'g'=>seq.count('g'),'t'=>seq.count('t')}
!     p randomseq = Bio::Sequence::NA.randomize(counts)  # reshuffle sequence with same freq.
  
  The p, print and puts methods are standard Ruby ways of outputting to
--- 115,122 ----
      puts seq.complement.translate       # translation of complemental strand
  
!     # reshuffle sequence with same frequencies:
!     counts = {'a'=>seq.count('a'),'c'=>seq.count('c'),
!               'g'=>seq.count('g'),'t'=>seq.count('t')}
!     p randomseq = Bio::Sequence::NA.randomize(counts)  
  
  The p, print and puts methods are standard Ruby ways of outputting to
***************
*** 265,269 ****
        print ">#{gb.accession} "         # Accession
        puts gb.definition                # Definition
!       puts gb.naseq                     # Nucleic acid sequence (Bio::Sequence::NA object)
      end
  
--- 267,272 ----
        print ">#{gb.accession} "         # Accession
        puts gb.definition                # Definition
!       puts gb.naseq                     # Nucleic acid sequence 
!                                         # (Bio::Sequence::NA object)
      end
  
***************
*** 387,391 ****
      aaseq.splicing('21..119')
  
- (EDITOR's NOTE: why use STRINGs here?)
  
  === More databases
--- 390,393 ----
***************
*** 494,498 ****
  and cut a sequence with an enzyme follow up with:
  
!    res = seq.cut_with_enzyme('EcoRII', {:max_permutations => 0}, {:view_ranges => true})
     if res.kind_of? Symbol #error
        err = Err.find_by_code(res.to_s)
--- 496,501 ----
  and cut a sequence with an enzyme follow up with:
  
!    res = seq.cut_with_enzyme('EcoRII', {:max_permutations => 0}, 
!      {:view_ranges => true})
     if res.kind_of? Symbol #error
        err = Err.find_by_code(res.to_s)
***************
*** 529,534 ****
  fasta34. FASTA can be downloaded from ftp://ftp.virginia.edu/pub/fasta/).
  First, you must prepare your FASTA-formatted database sequence file
! target.pep and FASTA-formatted query.pep.  (TRANSLATOR'S NOTE: I think
! we should provide sample data to readers.)
  
      #!/usr/bin/env ruby
--- 532,536 ----
  fasta34. FASTA can be downloaded from ftp://ftp.virginia.edu/pub/fasta/).
  First, you must prepare your FASTA-formatted database sequence file
! target.pep and FASTA-formatted query.pep. 
  
      #!/usr/bin/env ruby
***************
*** 536,547 ****
      require 'bio'
  
!     # Creates FASTA factory object ("ssearch" instead of "fasta34" can also work)
      factory = Bio::Fasta.local('fasta34', ARGV.pop)
      (EDITOR's NOTE: not consistent pop command)
  
-     # Reads FASTA-formatted files (TRANSLATOR'S NOTE: something wrong in Japanese text)
      ff = Bio::FlatFile.new(Bio::FastaFormat, ARGF)
  
!     # Iterates over each entry. the variable "entry" is a Bio::FastaFormat object.
      ff.each do |entry|
        # shows definition line (begins with '>') to the standard error output
--- 538,550 ----
      require 'bio'
  
!     # Creates FASTA factory object ("ssearch" instead of 
!     # "fasta34" can also work)
      factory = Bio::Fasta.local('fasta34', ARGV.pop)
      (EDITOR's NOTE: not consistent pop command)
  
      ff = Bio::FlatFile.new(Bio::FastaFormat, ARGF)
  
!     # Iterates over each entry. the variable "entry" is a 
!     # Bio::FastaFormat object:
      ff.each do |entry|
        # shows definition line (begins with '>') to the standard error output
***************
*** 555,559 ****
          # If E-value is smaller than 0.0001
          if hit.evalue < 0.0001
!           # shows identifier of query and hit, E-value, start and end positions of homologous region (TRANSLATOR'S NOTE: should I change Japanese document?)
            print "#{hit.query_id} : evalue #{hit.evalue}\t#{hit.target_id} at "
            p hit.lap_at
--- 558,563 ----
          # If E-value is smaller than 0.0001
          if hit.evalue < 0.0001
!           # shows identifier of query and hit, E-value, start and 
!           # end positions of homologous region 
            print "#{hit.query_id} : evalue #{hit.evalue}\t#{hit.target_id} at "
            p hit.lap_at
***************
*** 569,573 ****
  FASTA many times easily. Instead of using Fasta#query method,
  Bio::Sequence#fasta method can be used.
- (TRANSLATOR'S NOTE: Bio::Sequence#fasta are not so frequently used.)
  
      seq = ">test seq\nYQVLEEIGRGSFGSVRKVIHIPTKKLLVRKDIKYGHMNSKE"
--- 573,576 ----
***************
*** 585,589 ****
  with the Report object. For example, getting information for hits:
  
- 
      report.each do |hit|
        puts hit.evalue           # E-value
--- 588,591 ----
***************
*** 594,606 ****
        puts hit.query_def        # definition(comment line) of query sequence
        puts hit.query_len        # length of query sequence
!       puts hit.query_seq        # query sequence (TRANSLATOR'S NOTE: sequence of homologous region of query sequence)
        puts hit.target_id        # identifier of hit sequence
        puts hit.target_def       # definition(comment line) of hit sequence
        puts hit.target_len       # length of hit sequence
!       puts hit.target_seq       # hit sequence (TRANSLATOR'S NOTE: sequence of homologous region of hit sequence)
!       puts hit.query_start      # start position of homologous region in query sequence
!       puts hit.query_end        # end position of homologous region in query sequence
!       puts hit.target_start     # start posiotion of homologous region in hit(target) sequence
!       puts hit.target_end       # end position of homologous region in hit(target) sequence
        puts hit.lap_at           # array of above four numbers
      end
--- 596,612 ----
        puts hit.query_def        # definition(comment line) of query sequence
        puts hit.query_len        # length of query sequence
!       puts hit.query_seq        # sequence of homologous region
        puts hit.target_id        # identifier of hit sequence
        puts hit.target_def       # definition(comment line) of hit sequence
        puts hit.target_len       # length of hit sequence
!       puts hit.target_seq       # hit of homologous region of hit sequence
!       puts hit.query_start      # start position of homologous 
!                                 # region in query sequence
!       puts hit.query_end        # end position of homologous region 
!                                 # in query sequence
!       puts hit.target_start     # start posiotion of homologous region 
!                                 # in hit(target) sequence
!       puts hit.target_end       # end position of homologous region 
!                                 # in hit(target) sequence
        puts hit.lap_at           # array of above four numbers
      end
***************
*** 695,717 ****
  
      report.each do |hit|
!       puts hit.bit_score        # bit score (*)
!       puts hit.query_seq        # query sequence (TRANSLATOR'S NOTE: sequence of homologous region of query sequence)
!       puts hit.midline          # middle line string of alignment of homologous region (*)
!       puts hit.target_seq       # hit sequence (TRANSLATOR'S NOTE: sequence of homologous region of query sequence)
  
!       puts hit.evalue           # E-value
!       puts hit.identity         # % identity
!       puts hit.overlap          # length of overlapping region
!       puts hit.query_id         # identifier of query sequence
!       puts hit.query_def        # definition(comment line) of query sequence
!       puts hit.query_len        # length of query sequence
!       puts hit.target_id        # identifier of hit sequence
!       puts hit.target_def       # definition(comment line) of hit sequence
!       puts hit.target_len       # length of hit sequence
!       puts hit.query_start      # start position of homologous region in query sequence
!       puts hit.query_end        # end position of homologous region in query sequence
!       puts hit.target_start     # start position of homologous region in hit(target) sequence
!       puts hit.target_end       # end position of homologous region in hit(target) sequence
!       puts hit.lap_at           # array of above four numbers
      end
  
--- 701,723 ----
  
      report.each do |hit|
!       puts hit.bit_score       
!       puts hit.query_seq       
!       puts hit.midline         
!       puts hit.target_seq      
  
!       puts hit.evalue          
!       puts hit.identity        
!       puts hit.overlap         
!       puts hit.query_id        
!       puts hit.query_def       
!       puts hit.query_len       
!       puts hit.target_id       
!       puts hit.target_def      
!       puts hit.target_len      
!       puts hit.query_start     
!       puts hit.query_end       
!       puts hit.target_start    
!       puts hit.target_end      
!       puts hit.lap_at          
      end
  
***************
*** 1171,1175 ****
  == KEGG API
  
! Please refer to KEGG_API.rd.ja (TRANSLATOR'S NOTE: English version: ((<URL:http://www.genome.jp/kegg/soap/doc/keggapi_manual.html>)) ) and
  
    * ((<URL:http://www.genome.jp/kegg/soap/>))
--- 1177,1181 ----
  == KEGG API
  
! Please refer to KEGG_API.rd.ja (English version: ((<URL:http://www.genome.jp/kegg/soap/doc/keggapi_manual.html>)) ) and
  
    * ((<URL:http://www.genome.jp/kegg/soap/>))


From pjotr at dev.open-bio.org  Sun Feb  3 12:17:59 2008
From: pjotr at dev.open-bio.org (Pjotr Prins)
Date: Sun, 03 Feb 2008 17:17:59 -0000
Subject: [BioRuby-cvs] bioruby/doc Tutorial.rd,1.16,1.17
Message-ID: <200802031717.m13HHoa6015904@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/doc
In directory dev.open-bio.org:/tmp/cvs-serv15881/doc

Modified Files:
	Tutorial.rd 
Log Message:
More doctests in Tutorial.rd

Index: Tutorial.rd
===================================================================
RCS file: /home/repository/bioruby/bioruby/doc/Tutorial.rd,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** Tutorial.rd	2 Feb 2008 14:15:08 -0000	1.16
--- Tutorial.rd	3 Feb 2008 17:17:48 -0000	1.17
***************
*** 13,16 ****
--- 13,17 ----
  
  =begin
+ #doctest Testing bioruby
  
  = BioRuby Tutorial
***************
*** 64,68 ****
  following command
  
!   ./bin/bioruby
  
  and you should see a prompt
--- 65,70 ----
  following command
  
!   ./bin/bioruby  or
!   ruby -I lib bin/bioruby
  
  and you should see a prompt
***************
*** 73,80 ****
  
    bioruby> seq = Bio::Sequence::NA.new("atgcatgcaaaa")
!   bioruby> puts seq
!   atgcatgcaaaa
!   bioruby> puts seq.complement
!   ttttgcatgcat
  
  == Working with nucleic / amino acid sequences (Bio::Sequence class)
--- 75,82 ----
  
    bioruby> seq = Bio::Sequence::NA.new("atgcatgcaaaa")
!   ==> "atgcatgcaaaa"
! 
!   bioruby> seq.complement
!   ==> "ttttgcatgcat"
  
  == Working with nucleic / amino acid sequences (Bio::Sequence class)
***************
*** 89,122 ****
  defined in codontable.rb).
  
  
!     #!/usr/bin/env ruby
! 
!     require 'bio'
! 
!     seq = Bio::Sequence::NA.new("atgcatgcaaaa")
! 
!     puts seq                            # original sequence
!     puts seq.complement                 # complemental sequence (Bio::Sequence::NA object)
!     puts seq.subseq(3,8)                # gets subsequence of positions 3 to 8
  
!     p seq.gc_percent                    # GC percent (BioRuby 0.6.X: Float, BioRuby 0.7 or later: Integer)
!     p seq.composition                   # nucleic acid compositions (Hash)
  
!     puts seq.translate                  # translation (Bio::Sequence::AA object)
!     puts seq.translate(2)               # translation from frame 2 (default is frame 1)
!     puts seq.translate(1,11)            # using codon table No.11 
!                                         # (see http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi)
  
!     p seq.translate.codes               # shows three-letter codes (Array)
!     p seq.translate.names               # shows amino acid names (Array)
!     p seq.translate.composition         # amino acid compositions (Hash)
!     p seq.translate.molecular_weight    # calculating molecular weight (Float)
  
!     puts seq.complement.translate       # translation of complemental strand
  
-     # reshuffle sequence with same frequencies:
-     counts = {'a'=>seq.count('a'),'c'=>seq.count('c'),
-               'g'=>seq.count('g'),'t'=>seq.count('t')}
-     p randomseq = Bio::Sequence::NA.randomize(counts)  
  
  The p, print and puts methods are standard Ruby ways of outputting to
--- 91,136 ----
  defined in codontable.rb).
  
+   bioruby> seq = Bio::Sequence::NA.new("atgcatgcaaaa")
+   ==> "atgcatgcaaaa"
  
!   # complemental sequence (Bio::Sequence::NA object)
!   bioruby> seq.complement
!   ==> "ttttgcatgcat"
  
!   bioruby> seq.subseq(3,8) # gets subsequence of positions 3 to 8
!   ==> "gcatgc"
!   bioruby> seq.gc_percent 
!   ==> 33
!   bioruby> seq.composition 
!   ==> {"a"=>6, "c"=>2, "g"=>2, "t"=>2}
!   bioruby> seq.translate 
!   ==> "MHAK"
!   bioruby> seq.translate(2)        # translate from frame 2
!   ==> "CMQ"
!   bioruby> seq.translate(1,11)     # codon table 11
!   ==> "MHAK"
!   bioruby> seq.translate.codes
!   ==> ["Met", "His", "Ala", "Lys"]
!   bioruby> seq.translate.names
!   ==> ["methionine", "histidine", "alanine", "lysine"]
!   bioruby>  seq.translate.composition
!   ==> {"K"=>1, "A"=>1, "M"=>1, "H"=>1}
!   bioruby> seq.translate.molecular_weight
!   ==> 485.605
!   bioruby> seq.complement.translate
!   ==> "FCMH"
  
! get a random sequence with the same NA count:
  
!   bioruby> counts = {'a'=>seq.count('a'),'c'=>seq.count('c'),'g'=>seq.count('g'),'t'=>seq.count('t')}
!   ==> {"a"=>6, "c"=>2, "g"=>2, "t"=>2}
!   bioruby!> randomseq = Bio::Sequence::NA.randomize(counts) 
!   ==!> "aaacatgaagtc"
  
!   bioruby!> print counts
! a6c2g2t2  
!   bioruby!> p counts
! {"a"=>6, "c"=>2, "g"=>2, "t"=>2}
  
  
  The p, print and puts methods are standard Ruby ways of outputting to
***************
*** 140,152 ****
  has index 0, for example:
  
!   s = 'abc'
!   puts s[0].chr
! 
!   >a
! 
!   puts s[0..1]
! 
!   >ab
! 
  
  So when using String methods, you should subtract 1 from positions
--- 154,163 ----
  has index 0, for example:
  
!   bioruby> s = 'abc'
!   ==> "abc"
!   bioruby> s[0].chr
!   ==> "a"
!   bioruby> s[0..1]
!   ==> "ab"
  
  So when using String methods, you should subtract 1 from positions
***************
*** 160,169 ****
  through a variable named +s+.
  
! * Shows average percentage of GC content for 100 bases (stepping
! the default one base at a time)
  
!     seq.window_search(100) do |s|
!       puts s.gc_percent
!     end
  
  Since the class of each subsequence is the same as original sequence
--- 171,182 ----
  through a variable named +s+.
  
! * Shows average percentage of GC content for 20 bases (stepping the default one base at a time)
  
! bioruby> seq = Bio::Sequence::NA.new("atgcatgcaattaagctaatcccaattagatcatcccgatcatcaaaaaaaaaa")
!   ==> "atgcatgcaattaagctaatcccaattagatcatcccgatcatcaaaaaaaaaa"
! 
!   bioruby>  seq.window_search(20) { |s| print s.gc_percent,',' } 
! 30,35,40,40,35,35,35,30,25,30,30,30,35,35,35,35,35,40,45,45,45,45,40,35,40,40,40,40,40,35,35,35,30,30,30,  ==> ""
!  
  
  Since the class of each subsequence is the same as original sequence
***************
*** 1165,1168 ****
--- 1178,1192 ----
  included - with output)
  
+ == Unit testing and doctests
+ 
+ BioRuby comes with an extensive testing framework with over 1300 tests and 2700
+ assertions. To run the unit tests:
+ 
+   cd test
+   ruby runner.rb
+ 
+ We have also started with doctest for Ruby. We are porting the examples
+ in this tutorial to doctest - more info upcoming.
+ 
  == Further reading
  


From pjotr at dev.open-bio.org  Tue Feb  5 07:01:26 2008
From: pjotr at dev.open-bio.org (Pjotr Prins)
Date: Tue, 05 Feb 2008 12:01:26 -0000
Subject: [BioRuby-cvs] bioruby/doc Tutorial.rd,1.17,1.18
Message-ID: <200802051201.m15C1JTf032112@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/doc
In directory dev.open-bio.org:/tmp/cvs-serv32092/doc

Modified Files:
	Tutorial.rd 
Log Message:
Minor tweak to Tutorial.rd

Index: Tutorial.rd
===================================================================
RCS file: /home/repository/bioruby/bioruby/doc/Tutorial.rd,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -d -r1.17 -r1.18
*** Tutorial.rd	3 Feb 2008 17:17:48 -0000	1.17
--- Tutorial.rd	5 Feb 2008 12:01:16 -0000	1.18
***************
*** 129,135 ****
  
    bioruby!> print counts
! a6c2g2t2  
    bioruby!> p counts
! {"a"=>6, "c"=>2, "g"=>2, "t"=>2}
  
  
--- 129,135 ----
  
    bioruby!> print counts
!   a6c2g2t2  
    bioruby!> p counts
!   {"a"=>6, "c"=>2, "g"=>2, "t"=>2}
  
  
***************
*** 173,183 ****
  * Shows average percentage of GC content for 20 bases (stepping the default one base at a time)
  
! bioruby> seq = Bio::Sequence::NA.new("atgcatgcaattaagctaatcccaattagatcatcccgatcatcaaaaaaaaaa")
    ==> "atgcatgcaattaagctaatcccaattagatcatcccgatcatcaaaaaaaaaa"
  
    bioruby>  seq.window_search(20) { |s| print s.gc_percent,',' } 
! 30,35,40,40,35,35,35,30,25,30,30,30,35,35,35,35,35,40,45,45,45,45,40,35,40,40,40,40,40,35,35,35,30,30,30,  ==> ""
   
- 
  Since the class of each subsequence is the same as original sequence
  (Bio::Sequence::NA or Bio::Sequence::AA or Bio::Sequence), you can
--- 173,182 ----
  * Shows average percentage of GC content for 20 bases (stepping the default one base at a time)
  
!   bioruby> seq = Bio::Sequence::NA.new("atgcatgcaattaagctaatcccaattagatcatcccgatcatcaaaaaaaaaa")
    ==> "atgcatgcaattaagctaatcccaattagatcatcccgatcatcaaaaaaaaaa"
  
    bioruby>  seq.window_search(20) { |s| print s.gc_percent,',' } 
!   30,35,40,40,35,35,35,30,25,30,30,30,35,35,35,35,35,40,45,45,45,45,40,35,40,40,40,40,40,35,35,35,30,30,30,  ==> ""
   
  Since the class of each subsequence is the same as original sequence
  (Bio::Sequence::NA or Bio::Sequence::AA or Bio::Sequence), you can


From pjotr at dev.open-bio.org  Tue Feb  5 07:11:20 2008
From: pjotr at dev.open-bio.org (Pjotr Prins)
Date: Tue, 05 Feb 2008 12:11:20 -0000
Subject: [BioRuby-cvs] bioruby/sample gb2fasta.rb,0.5,0.6
Message-ID: <200802051211.m15CBDam032291@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/sample
In directory dev.open-bio.org:/tmp/cvs-serv32271/sample

Modified Files:
	gb2fasta.rb 
Log Message:
Fixed broken require in gb2fasta example

Index: gb2fasta.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/sample/gb2fasta.rb,v
retrieving revision 0.5
retrieving revision 0.6
diff -C2 -d -r0.5 -r0.6
*** gb2fasta.rb	23 Jul 2002 04:51:24 -0000	0.5
--- gb2fasta.rb	5 Feb 2008 12:11:11 -0000	0.6
***************
*** 19,24 ****
  #
  
! require 'bio/io/flatfile'
! require 'bio/db/genbank'
  
  include Bio
--- 19,23 ----
  #
  
! require 'bio'
  
  include Bio


From pjotr at dev.open-bio.org  Wed Feb  6 11:26:05 2008
From: pjotr at dev.open-bio.org (Pjotr Prins)
Date: Wed, 06 Feb 2008 16:26:05 -0000
Subject: [BioRuby-cvs] bioruby/sample na2aa.rb,NONE,1.1
Message-ID: <200802061625.m16GPuIu005441@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/sample
In directory dev.open-bio.org:/tmp/cvs-serv5421

Added Files:
	na2aa.rb 
Log Message:
Simple example to translate any NA to AA fasta

--- NEW FILE: na2aa.rb ---
#!/usr/bin/env ruby
#
# translate.rb - translate any NA input into AA FASTA format
#
#   Copyright (C) 2008 KATAYAMA Toshiaki <k at bioruby.org> & Pjotr Prins
#
#  This program is free software; you can redistribute it and/or modify
#  it under the terms of the GNU General Public License as published by
#  the Free Software Foundation; either version 2 of the License, or
#  (at your option) any later version.
#
#  This program is distributed in the hope that it will be useful,
#  but WITHOUT ANY WARRANTY; without even the implied warranty of
#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#  GNU General Public License for more details.
#
#  $Id: na2aa.rb,v 1.1 2008/02/06 16:25:53 pjotr Exp $
#

require 'bio'
require 'pp'

include Bio

ARGV.each do | fn |
  Bio::FlatFile.auto(fn).each do | item |
    seq = Sequence::NA.new(item.data)
    aa = seq.translate
    aa.gsub!(/X/,'-')
    rec = Bio::FastaFormat.new('> '+item.definition+"\n"+aa)
    print rec
  end
end



From pjotr at dev.open-bio.org  Mon Feb 11 02:08:56 2008
From: pjotr at dev.open-bio.org (Pjotr Prins)
Date: Mon, 11 Feb 2008 07:08:56 -0000
Subject: [BioRuby-cvs] bioruby/doc Tutorial.rd,1.18,1.19
Message-ID: <200802110708.m1B78mwU007283@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/doc
In directory dev.open-bio.org:/tmp/cvs-serv7263/doc

Modified Files:
	Tutorial.rd 
Log Message:
Expanding on the Tutorial

Index: Tutorial.rd
===================================================================
RCS file: /home/repository/bioruby/bioruby/doc/Tutorial.rd,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** Tutorial.rd	5 Feb 2008 12:01:16 -0000	1.18
--- Tutorial.rd	11 Feb 2008 07:08:46 -0000	1.19
***************
*** 1,5 ****
  # This document is generated with a version of rd2html (part of Hiki)
  #
! # A possible test run could be from rdtool:
  #
  #   ruby -I lib ./bin/rd2 ~/cvs/opensource/bioruby/doc/Tutorial.rd
--- 1,5 ----
  # This document is generated with a version of rd2html (part of Hiki)
  #
! # A possible test run could be from rdtool (on Debian package rdtool)
  #
  #   ruby -I lib ./bin/rd2 ~/cvs/opensource/bioruby/doc/Tutorial.rd
***************
*** 10,14 ****
  ss=bioruby.css ~/cvs/opensource/bioruby/doc/Tutorial.rd > ~/bioruby.html
  #
! # A common problem is tabs in the text file!
  
  =begin
--- 10,23 ----
  ss=bioruby.css ~/cvs/opensource/bioruby/doc/Tutorial.rd > ~/bioruby.html
  #
! # in Debian:
! #
! #   rd2 -r rd/rd2html-lib  --with-css="/home/wrk/izip/cvs/opensource/bioruby/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css" Tutorial.rd > index.html
! #
! # A common problem is tabs in the text file! TABs are not allowed.
! #
! # To add tests run Toshiaki's bioruby shell and paste in the query plus
! # results.
! #
! # To run the embedded Ruby doctests you can get the doctest.rb from Pjotr.
  
  =begin
***************
*** 36,41 ****
  ((<here|URL:http://www.rubycentral.com/pickaxe/>)).
  
! For BioRuby you need to install
! Ruby and the BioRuby package on your computer.
  
  You can check whether Ruby is installed on your computer and what
--- 45,49 ----
  ((<here|URL:http://www.rubycentral.com/pickaxe/>)).
  
! For BioRuby you need to install Ruby and the BioRuby package on your computer
  
  You can check whether Ruby is installed on your computer and what
***************
*** 80,83 ****
--- 88,95 ----
    ==> "ttttgcatgcat"
  
+ See the the Bioruby shell section below for more tweaking. If you have trouble running
+ examples also check the section below on trouble shooting. You can also post a 
+ question to the mailing list. BioRuby developers usually try to help.
+ 
  == Working with nucleic / amino acid sequences (Bio::Sequence class)
  
***************
*** 171,181 ****
  through a variable named +s+.
  
! * Shows average percentage of GC content for 20 bases (stepping the default one base at a time)
  
    bioruby> seq = Bio::Sequence::NA.new("atgcatgcaattaagctaatcccaattagatcatcccgatcatcaaaaaaaaaa")
    ==> "atgcatgcaattaagctaatcccaattagatcatcccgatcatcaaaaaaaaaa"
  
!   bioruby>  seq.window_search(20) { |s| print s.gc_percent,',' } 
!   30,35,40,40,35,35,35,30,25,30,30,30,35,35,35,35,35,40,45,45,45,45,40,35,40,40,40,40,40,35,35,35,30,30,30,  ==> ""
   
  Since the class of each subsequence is the same as original sequence
--- 183,195 ----
  through a variable named +s+.
  
! * Show average percentage of GC content for 20 bases (stepping the default one base at a time)
  
    bioruby> seq = Bio::Sequence::NA.new("atgcatgcaattaagctaatcccaattagatcatcccgatcatcaaaaaaaaaa")
    ==> "atgcatgcaattaagctaatcccaattagatcatcccgatcatcaaaaaaaaaa"
  
!   bioruby> a=[]; seq.window_search(20) { |s| a.push s.gc_percent } 
!   bioruby> a
!   ==> [30, 35, 40, 40, 35, 35, 35, 30, 25, 30, 30, 30, 35, 35, 35, 35, 35, 40, 45, 45, 45, 45, 40, 35, 40, 40, 40, 40, 40, 35, 35, 35, 30, 30, 30]
! 
   
  Since the class of each subsequence is the same as original sequence
***************
*** 185,191 ****
  * Shows translation results for 15 bases shifting a codon at a time
  
!     seq.window_search(15, 3) do |s|
!       puts s.translate
!     end
  
  Finally, the window_search method returns the last leftover
--- 199,209 ----
  * Shows translation results for 15 bases shifting a codon at a time
  
!   bioruby> a = []
!   bioruby> seq.window_search(15, 3) do |s|
!   bioruby>   a.push s.translate
!   bioruby> end
!   bioruby> a
!   ==> ["MHAIK", "HAIKL", "AIKLI", "IKLIP", "KLIPI", "LIPIR", "IPIRS", "PIRSS", "IRSSR", "RSSRS", "SSRSS", "SRSSK", "RSSKK", "SSKKK"]
! 
  
  Finally, the window_search method returns the last leftover
***************
*** 193,206 ****
  
  * Divide a genome sequence into sections of 10000bp and
!   output FASTA formatted sequences. The 1000bp at the start and end of
!   each subsequence overlapped. At the 3' end of the sequence the
!   leftover subsequence shorter than 10000bp is also added
  
      i = 1
      remainder = seq.window_search(10000, 9000) do |s|
!       puts s.to_fasta("segment #{i}", 60)
        i += 1
      end
!     puts remainder.to_fasta("segment #{i}", 60)
  
  If you don't want the overlapping window, set window size and stepping
--- 211,227 ----
  
  * Divide a genome sequence into sections of 10000bp and
!   output FASTA formatted sequences (line width 60 chars). The 1000bp at the
!   start and end of each subsequence overlapped. At the 3' end of the sequence
!   the leftover is also added:
  
      i = 1
+     textwidth=60
      remainder = seq.window_search(10000, 9000) do |s|
!       puts s.to_fasta("segment #{i}", textwidth)
        i += 1
      end
!     if remainder
!       puts remainder.to_fasta("segment #{i}", textwidth) 
!     end
  
  If you don't want the overlapping window, set window size and stepping
***************
*** 211,224 ****
  * Count the codon usage
  
!     codon_usage = Hash.new(0)
!     seq.window_search(3, 3) do |s|
!       codon_usage[s] += 1
!     end
  
  * Calculate molecular weight for each 10-aa peptide (or 10-nt nucleic acid)
  
!     seq.window_search(10, 10) do |s|
!       puts s.molecular_weight
!     end
  
  In most cases, sequences are read from files or retrieved from databases.
--- 232,251 ----
  * Count the codon usage
  
!   bioruby> codon_usage = Hash.new(0)
!   bioruby> seq.window_search(3, 3) do |s|
!   bioruby>   codon_usage[s] += 1
!   bioruby> end
!   bioruby> codon_usage
!   ==> {"cat"=>1, "aaa"=>3, "cca"=>1, "att"=>2, "aga"=>1, "atc"=>1, "cta"=>1, "gca"=>1, "cga"=>1, "tca"=>3, "aag"=>1, "tcc"=>1, "atg"=>1}
! 
  
  * Calculate molecular weight for each 10-aa peptide (or 10-nt nucleic acid)
  
!   bioruby> a = []
!   bioruby> seq.window_search(10, 10) do |s|
!   bioruby>   a.push s.molecular_weight
!   bioruby> end
!   bioruby> a
!   ==> [3096.2062, 3086.1962, 3056.1762, 3023.1262, 3073.2262]
  
  In most cases, sequences are read from files or retrieved from databases.
***************
*** 246,249 ****
--- 273,280 ----
      % ruby na2aa.rb my_naseq.txt
  
+ or use a pipe!
+ 
+     % cat my_naseq.txt|ruby na2aa.rb
+ 
  Outputs
  
***************
*** 254,259 ****
      % ruby -r bio -e 'p Bio::Sequence::NA.new($<.read).translate' my_naseq.txt
  
! In the next section we will retrieve data from databases instead of
! using raw sequence files.
  
  == Parsing GenBank data (Bio::GenBank class)
--- 285,291 ----
      % ruby -r bio -e 'p Bio::Sequence::NA.new($<.read).translate' my_naseq.txt
  
! In the next section we will retrieve data from databases instead of using raw
! sequence files. One generic example of the above can be found in
! ./sample/na2aa.rb.
  
  == Parsing GenBank data (Bio::GenBank class)
***************
*** 460,474 ****
  Array and BioPerl's Bio::SimpleAlign.  A very simple example is:
  
!   require 'bio'
! 
!   seqs = [ 'atgca', 'aagca', 'acgca', 'acgcg' ]
!   seqs = seqs.collect{ |x| Bio::Sequence::NA.new(x) }
! 
    # creates alignment object
!   a = Bio::Alignment.new(seqs)
! 
!   # shows consensus sequence
!   p a.consensus             # ==> "a?gc?"
! 
    # shows IUPAC consensus
    p a.consensus_iupac       # ==> "ahgcr"
--- 492,501 ----
  Array and BioPerl's Bio::SimpleAlign.  A very simple example is:
  
!   bioruby> seqs = [ 'atgca', 'aagca', 'acgca', 'acgcg' ]
!   bioruby> seqs = seqs.collect{ |x| Bio::Sequence::NA.new(x) }
    # creates alignment object
!   bioruby> a = Bio::Alignment.new(seqs)
!   bioruby> a.consensus 
!   ==> "xa?gc?"
    # shows IUPAC consensus
    p a.consensus_iupac       # ==> "ahgcr"
***************
*** 1168,1179 ****
  == The BioRuby example programs
  
! Some sample programs are stored in samples/ directry.
! Some programs are obsolete. Since samples are not enough,
! practical and interesting samples are welcome.
! 
! to be written...
  
! (EDITOR's NOTE: I would like some examples automatically
! included - with output)
  
  == Unit testing and doctests
--- 1195,1201 ----
  == The BioRuby example programs
  
! Some sample programs are stored in ./samples/ directory. Run for example:
  
!   ./sample/na2aa.rb test/data/fasta/example1.txt 
  
  == Unit testing and doctests
***************
*** 1195,1198 ****
--- 1217,1242 ----
  ((<URL:http://bioruby.org/rdoc/>)).
  
+ == BioRuby Shell
+ 
+ The BioRuby shell implementation you find in ./lib/bio/shell. It is very interesting
+ as it uses IRB (the Ruby intepreter) which is a powerful environment described in
+ ((<Programming Ruby's irb chapter|URL:http://ruby-doc.org/docs/ProgrammingRuby/html/irb.html>)). IRB commands can directly be typed in the shell, e.g.
+ 
+   bioruby!> IRB.conf[:PROMPT_MODE]
+   ==!> :PROMPT_C
+ 
+ optionally you also may want to install the optional Ruby readline support -
+ with Debian libreadline-ruby. To edit a previous line you may have to press
+ line down (arrow down) first.
+ 
+ = Helpful tools
+ 
+ Apart from rdoc you may also want to use rtags - which allows jumping around
+ source code by clicking on class and method names. 
+ 
+   cd bioruby/lib
+   rtags -R --vi
+ 
+ For a tutorial see ((<URL:http://rtags.rubyforge.org/>))
  
  = APPENDIX
***************
*** 1227,1230 ****
--- 1271,1283 ----
  carefully that come with each package.
  
+ == Trouble shooting
+ 
+ * Error: in `require': no such file to load -- bio (LoadError)
+ 
+ Ruby fails to find the BioRuby libraries - add it to the RUBYLIB path, or pass
+ it to the interpeter. For example:
+ 
+   ruby -I~/cvs/bioruby/lib yourprogram.rb
+ 
  == Modifying this page
  


From pjotr at dev.open-bio.org  Mon Feb 11 03:03:36 2008
From: pjotr at dev.open-bio.org (Pjotr Prins)
Date: Mon, 11 Feb 2008 08:03:36 -0000
Subject: [BioRuby-cvs] bioruby/doc Tutorial.rd,1.19,1.20
Message-ID: <200802110803.m1B83TYu007417@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/doc
In directory dev.open-bio.org:/tmp/cvs-serv7397

Modified Files:
	Tutorial.rd 
Log Message:
Minor adjustments to Tutorial

Index: Tutorial.rd
===================================================================
RCS file: /home/repository/bioruby/bioruby/doc/Tutorial.rd,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -d -r1.19 -r1.20
*** Tutorial.rd	11 Feb 2008 07:08:46 -0000	1.19
--- Tutorial.rd	11 Feb 2008 08:03:27 -0000	1.20
***************
*** 497,519 ****
    bioruby> a = Bio::Alignment.new(seqs)
    bioruby> a.consensus 
!   ==> "xa?gc?"
    # shows IUPAC consensus
!   p a.consensus_iupac       # ==> "ahgcr"
! 
    # iterates over each seq
    a.each { |x| p x }
!     # ==>
!     #    "atgca"
!     #    "aagca"
!     #    "acgca"
!     #    "acgcg"
    # iterates over each site
    a.each_site { |x| p x }
!     # ==>
!     #    ["a", "a", "a", "a"]
!     #    ["t", "a", "c", "c"]
!     #    ["g", "g", "g", "g"]
!     #    ["c", "c", "c", "c"]
!     #    ["a", "a", "a", "g"]
  
    # doing alignment by using CLUSTAL W.
--- 497,519 ----
    bioruby> a = Bio::Alignment.new(seqs)
    bioruby> a.consensus 
!   ==> "a?gc?"
    # shows IUPAC consensus
!   a.consensus_iupac 
!   ==> "ahgcr"
    # iterates over each seq
    a.each { |x| p x }
!   # ==>
!   #    "atgca"
!   #    "aagca"
!   #    "acgca"
!   #    "acgcg"
    # iterates over each site
    a.each_site { |x| p x }
!   # ==>
!   #    ["a", "a", "a", "a"]
!   #    ["t", "a", "c", "c"]
!   #    ["g", "g", "g", "g"]
!   #    ["c", "c", "c", "c"]
!   #    ["a", "a", "a", "g"]
  
    # doing alignment by using CLUSTAL W.


From pjotr at dev.open-bio.org  Wed Feb 13 03:04:41 2008
From: pjotr at dev.open-bio.org (Pjotr Prins)
Date: Wed, 13 Feb 2008 08:04:41 -0000
Subject: [BioRuby-cvs] bioruby/doc Tutorial.rd,1.20,1.21
Message-ID: <200802130804.m1D84XQC015600@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/doc
In directory dev.open-bio.org:/tmp/cvs-serv15580

Modified Files:
	Tutorial.rd 
Log Message:
Tutorial

Index: Tutorial.rd
===================================================================
RCS file: /home/repository/bioruby/bioruby/doc/Tutorial.rd,v
retrieving revision 1.20
retrieving revision 1.21
diff -C2 -d -r1.20 -r1.21
*** Tutorial.rd	11 Feb 2008 08:03:27 -0000	1.20
--- Tutorial.rd	13 Feb 2008 08:04:30 -0000	1.21
***************
*** 183,187 ****
  through a variable named +s+.
  
! * Show average percentage of GC content for 20 bases (stepping the default one base at a time)
  
    bioruby> seq = Bio::Sequence::NA.new("atgcatgcaattaagctaatcccaattagatcatcccgatcatcaaaaaaaaaa")
--- 183,187 ----
  through a variable named +s+.
  
! Show average percentage of GC content for 20 bases (stepping the default one base at a time)
  
    bioruby> seq = Bio::Sequence::NA.new("atgcatgcaattaagctaatcccaattagatcatcccgatcatcaaaaaaaaaa")
***************
*** 197,201 ****
  use all methods on the subsequence. For example,
  
! * Shows translation results for 15 bases shifting a codon at a time
  
    bioruby> a = []
--- 197,201 ----
  use all methods on the subsequence. For example,
  
! Shows translation results for 15 bases shifting a codon at a time
  
    bioruby> a = []
***************
*** 210,217 ****
  subsequence. This allows for example
  
! * Divide a genome sequence into sections of 10000bp and
!   output FASTA formatted sequences (line width 60 chars). The 1000bp at the
!   start and end of each subsequence overlapped. At the 3' end of the sequence
!   the leftover is also added:
  
      i = 1
--- 210,217 ----
  subsequence. This allows for example
  
! Divide a genome sequence into sections of 10000bp and
! output FASTA formatted sequences (line width 60 chars). The 1000bp at the
! start and end of each subsequence overlapped. At the 3' end of the sequence
! the leftover is also added:
  
      i = 1
***************
*** 230,234 ****
  Other examples
  
! * Count the codon usage
  
    bioruby> codon_usage = Hash.new(0)
--- 230,234 ----
  Other examples
  
! Count the codon usage
  
    bioruby> codon_usage = Hash.new(0)
***************
*** 240,244 ****
  
  
! * Calculate molecular weight for each 10-aa peptide (or 10-nt nucleic acid)
  
    bioruby> a = []
--- 240,244 ----
  
  
! Calculate molecular weight for each 10-aa peptide (or 10-nt nucleic acid)
  
    bioruby> a = []
***************
*** 399,408 ****
      end
  
! * Note: In this example Feature#assoc method makes a Hash from a
!   feature object. It is useful because you can get data from the hash
!   by using qualifiers as keys.
!   (But there is a risk some information is lost when two or more
!   qualifiers are the same. Therefore an Array is returned by
!   Feature#feature)
  
  Bio::Sequence#splicing splices subsequence from nucleic acid sequence
--- 399,408 ----
      end
  
! Note: In this example Feature#assoc method makes a Hash from a
! feature object. It is useful because you can get data from the hash
! by using qualifiers as keys.
! (But there is a risk some information is lost when two or more
! qualifiers are the same. Therefore an Array is returned by
! Feature#feature)
  
  Bio::Sequence#splicing splices subsequence from nucleic acid sequence
***************
*** 418,426 ****
  bio/location.rb.
  
! * Splice according to location string used in a GenBank entry
  
      naseq.splicing('join(2035..2050,complement(1775..1818),13..345')
  
! * Generate Bio::Locations object and pass the splicing method
  
      locs = Bio::Locations.new('join((8298.8300)..10206,1..855)')
--- 418,426 ----
  bio/location.rb.
  
! Splice according to location string used in a GenBank entry
  
      naseq.splicing('join(2035..2050,complement(1775..1818),13..345')
  
! Generate Bio::Locations object and pass the splicing method
  
      locs = Bio::Locations.new('join((8298.8300)..10206,1..855)')
***************
*** 430,434 ****
  (Bio::Sequence::AA objects).
  
! * Splicing peptide from a protein (e.g. signal peptide)
  
      aaseq.splicing('21..119')
--- 430,434 ----
  (Bio::Sequence::AA objects).
  
! Splicing peptide from a protein (e.g. signal peptide)
  
      aaseq.splicing('21..119')


From k at dev.open-bio.org  Sat Feb  2 03:36:00 2008
From: k at dev.open-bio.org (Katayama Toshiaki)
Date: Sat, 02 Feb 2008 03:36:00 +0000
Subject: [BioRuby-cvs] bioruby ChangeLog,1.80,1.81
Message-ID: <200802020336.m123a0gr029664@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby
In directory dev.open-bio.org:/tmp/cvs-serv29660

Modified Files:
	ChangeLog 
Log Message:
* lib/bio/shell/rails/vendor/plugins/

The 'generators' directory is moved under the 'bioruby' subdirectory
so that 'bioruby --rails' command can work with Rails 2.x series
in addition to the Rails 1.2.x series.



Index: ChangeLog
===================================================================
RCS file: /home/repository/bioruby/bioruby/ChangeLog,v
retrieving revision 1.80
retrieving revision 1.81
diff -C2 -d -r1.80 -r1.81
*** ChangeLog	9 Jan 2008 17:22:39 -0000	1.80
--- ChangeLog	2 Feb 2008 03:35:58 -0000	1.81
***************
*** 1,4 ****
--- 1,12 ----
  2008-01-10  Toshiaki Katayama <k at bioruby.org>
  
+ 	* lib/bio/shell/rails/vendor/plugins/
+ 
+ 	  The 'generators' directory is moved under the 'bioruby' subdirectory
+ 	  so that 'bioruby --rails' command can work with Rails 2.x series
+ 	  in addition to the Rails 1.2.x series.
+ 
+ 2008-01-10  Toshiaki Katayama <k at bioruby.org>
+ 
  	* lib/bio/io/hinv.rb
  



From k at dev.open-bio.org  Sat Feb  2 03:54:50 2008
From: k at dev.open-bio.org (Katayama Toshiaki)
Date: Sat, 02 Feb 2008 03:54:50 +0000
Subject: [BioRuby-cvs] bioruby ChangeLog,1.81,1.82
Message-ID: <200802020354.m123soGS029686@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby
In directory dev.open-bio.org:/tmp/cvs-serv29682

Modified Files:
	ChangeLog 
Log Message:
fix typo


Index: ChangeLog
===================================================================
RCS file: /home/repository/bioruby/bioruby/ChangeLog,v
retrieving revision 1.81
retrieving revision 1.82
diff -C2 -d -r1.81 -r1.82
*** ChangeLog	2 Feb 2008 03:35:58 -0000	1.81
--- ChangeLog	2 Feb 2008 03:54:48 -0000	1.82
***************
*** 1,3 ****
! 2008-01-10  Toshiaki Katayama <k at bioruby.org>
  
  	* lib/bio/shell/rails/vendor/plugins/
--- 1,3 ----
! 2008-02-02  Toshiaki Katayama <k at bioruby.org>
  
  	* lib/bio/shell/rails/vendor/plugins/



From ngoto at dev.open-bio.org  Tue Feb 12 02:13:34 2008
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Tue, 12 Feb 2008 02:13:34 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/blast format0.rb,1.25,1.26
Message-ID: <200802120213.m1C2DX5m009903@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/blast
In directory dev.open-bio.org:/tmp/cvs-serv9861/lib/bio/appl/blast

Modified Files:
	format0.rb 
Log Message:
* Bug fixes reported by Shuji Shigenobu.
  * Failed to parse query length for long query (>= 10000 letters)
    because comma is inserted for digit separator by blastall.
  * Failed to parse e-value for some BLASTX results


Index: format0.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast/format0.rb,v
retrieving revision 1.25
retrieving revision 1.26
diff -C2 -d -r1.25 -r1.26
*** format0.rb	27 Dec 2007 17:28:57 -0000	1.25
--- format0.rb	12 Feb 2008 02:13:31 -0000	1.26
***************
*** 265,270 ****
                  q << sc.scan(/.*/)
                  sc.skip(/\s*^ ?/)
!               end until !sc.rest or r = sc.skip(/ *\( *(\d+) *letters *\)\s*\z/)
!               @query_len = sc[1].to_i if r
                @query_def = q.join(' ')
              end
--- 265,270 ----
                  q << sc.scan(/.*/)
                  sc.skip(/\s*^ ?/)
!               end until !sc.rest or r = sc.skip(/ *\( *([\,\d]+) *letters *\)\s*\z/)
!               @query_len = sc[1].delete(',').to_i if r
                @query_def = q.join(' ')
              end
***************
*** 969,973 ****
                while sc.rest?
                  sc.skip(/\s*/)
!                 if sc.skip(/Expect(?:\(\d\))? *\= *([e\-\.\d]+)/) then
                    ev = sc[1].to_s
                    ev = '1' + ev if ev[0] == ?e
--- 969,973 ----
                while sc.rest?
                  sc.skip(/\s*/)
!                 if sc.skip(/Expect(?:\(\d+\))? *\= *([e\-\.\d]+)/) then
                    ev = sc[1].to_s
                    ev = '1' + ev if ev[0] == ?e



From ngoto at dev.open-bio.org  Tue Feb 12 05:32:25 2008
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Tue, 12 Feb 2008 05:32:25 +0000
Subject: [BioRuby-cvs] bioruby ChangeLog,1.82,1.83
Message-ID: <200802120532.m1C5WP5M011183@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby
In directory dev.open-bio.org:/tmp/cvs-serv11163

Modified Files:
	ChangeLog 
Log Message:
ChangeLog for lib/bio/appl/blast/format0.rb from 1.25 to 1.26.


Index: ChangeLog
===================================================================
RCS file: /home/repository/bioruby/bioruby/ChangeLog,v
retrieving revision 1.82
retrieving revision 1.83
diff -C2 -d -r1.82 -r1.83
*** ChangeLog	2 Feb 2008 03:54:48 -0000	1.82
--- ChangeLog	12 Feb 2008 05:32:23 -0000	1.83
***************
*** 1,2 ****
--- 1,11 ----
+ 2008-02-12  Naohisa Goto <ng at bioruby.org>
+ 
+ 	* lib/bio/appl/blast/format0.rb
+ 
+ 	  Fixed bugs: Failed to parse query length for long query
+ 	  (>= 10000 letters) as comma is inserted for digit separator
+ 	  by blastall; Failed to parse e-value for some BLASTX results.
+ 	  Thanks to Shuji Shigenobu who reported the bugs and sent patches.
+ 
  2008-02-02  Toshiaki Katayama <k at bioruby.org>
  



From ngoto at dev.open-bio.org  Wed Feb 13 10:28:20 2008
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Wed, 13 Feb 2008 10:28:20 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio sequence.rb,0.58,0.58.2.1
Message-ID: <200802131028.m1DASKHe017196@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv17175/lib/bio

Modified Files:
      Tag: BRANCH-biohackathon2008
	sequence.rb 
Log Message:
Added a new class method Bio::Sequence.read(str).


Index: sequence.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence.rb,v
retrieving revision 0.58
retrieving revision 0.58.2.1
diff -C2 -d -r0.58 -r0.58.2.1
*** sequence.rb	5 Apr 2007 23:35:39 -0000	0.58
--- sequence.rb	13 Feb 2008 10:28:16 -0000	0.58.2.1
***************
*** 334,337 ****
--- 334,356 ----
      @moltype = AA
    end
+ 
+   # Create a new Bio::Sequence object from a formatted string
+   # (GenBank, EMBL, fasta format, etc.)
+   #
+   #   s = Bio::Sequence.read(str)
+   # ---
+   # *Arguments*:
+   # * (required) _str_: string
+   # * (optional) _format_: format specification (class or nil)
+   # *Returns*:: Bio::Sequence object
+   def self.read(str, format = nil)
+     if format then
+       klass = format
+     else
+       klass = Bio::FlatFile::AutoDetect.default.guess(str)
+     end
+     obj = klass.new(str)
+     obj.to_biosequence
+   end
    
  end # Sequence



From ngoto at dev.open-bio.org  Thu Feb 14 03:13:48 2008
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Thu, 14 Feb 2008 03:13:48 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/sequence format.rb,1.4,1.4.2.1
Message-ID: <200802140313.m1E3Dm2s019722@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/sequence
In directory dev.open-bio.org:/tmp/cvs-serv19681/lib/bio/sequence

Modified Files:
      Tag: BRANCH-biohackathon2008
	format.rb 
Log Message:
* lib/bio/sequence.rb
  * changed to include Format module
* lib/bio/sequence/format.rb
  * fixed bug: incorrect refactoring


Index: format.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence/format.rb,v
retrieving revision 1.4
retrieving revision 1.4.2.1
diff -C2 -d -r1.4 -r1.4.2.1
*** format.rb	5 Apr 2007 23:35:41 -0000	1.4
--- format.rb	14 Feb 2008 03:13:46 -0000	1.4.2.1
***************
*** 18,23 ****
  module Bio
  
-   autoload :Sequence, 'bio/sequence'
- 
  class Sequence
  
--- 18,21 ----
***************
*** 127,131 ****
  
    def format_qualifiers(qualifiers, indent, width)
!     qualifiers.each do |qualifier|
        q = qualifier.qualifier
        v = qualifier.value.to_s
--- 125,129 ----
  
    def format_qualifiers(qualifiers, indent, width)
!     qualifiers.collect do |qualifier|
        q = qualifier.qualifier
        v = qualifier.value.to_s
***************
*** 134,138 ****
          lines = wrap('/' + q, width)
        elsif q == 'translation'
!         lines = fold('/' + q + '=' + val, width)
        else
          if v[/\D/]
--- 132,136 ----
          lines = wrap('/' + q, width)
        elsif q == 'translation'
!         lines = fold('/' + q + '=' + v, width)
        else
          if v[/\D/]
***************
*** 141,149 ****
            v = '"' + v + '"'
          end
!         lines = wrap('/' + q + '=' + val, width)
        end
  
!       return lines.gsub(/^/, indent)
!     end
    end
  
--- 139,148 ----
            v = '"' + v + '"'
          end
!         lines = wrap('/' + q + '=' + v, width)
        end
  
!       lines.gsub!(/^/, indent)
!       lines
!     end.join
    end
  



From ngoto at dev.open-bio.org  Thu Feb 14 03:13:48 2008
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Thu, 14 Feb 2008 03:13:48 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio sequence.rb,0.58.2.1,0.58.2.2
Message-ID: <200802140313.m1E3DmsN019717@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv19681/lib/bio

Modified Files:
      Tag: BRANCH-biohackathon2008
	sequence.rb 
Log Message:
* lib/bio/sequence.rb
  * changed to include Format module
* lib/bio/sequence/format.rb
  * fixed bug: incorrect refactoring


Index: sequence.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence.rb,v
retrieving revision 0.58.2.1
retrieving revision 0.58.2.2
diff -C2 -d -r0.58.2.1 -r0.58.2.2
*** sequence.rb	13 Feb 2008 10:28:16 -0000	0.58.2.1
--- sequence.rb	14 Feb 2008 03:13:46 -0000	0.58.2.2
***************
*** 71,74 ****
--- 71,75 ----
    autoload :Generic, 'bio/sequence/generic'
    autoload :Format,  'bio/sequence/format'
+   include Format
  
    # Create a new Bio::Sequence object
***************
*** 149,153 ****
    # *Returns*:: String object
    def output(style)
-     extend Bio::Sequence::Format
      case style
      when :fasta
--- 150,153 ----



From ngoto at dev.open-bio.org  Thu Feb 14 03:32:16 2008
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Thu, 14 Feb 2008 03:32:16 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/sequence format.rb,1.4.2.1,1.4.2.2
Message-ID: <200802140332.m1E3WGAu019905@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/sequence
In directory dev.open-bio.org:/tmp/cvs-serv19885/lib/bio/sequence

Modified Files:
      Tag: BRANCH-biohackathon2008
	format.rb 
Log Message:
in wrap(), the last "\n" should be added for non-empty string


Index: format.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence/format.rb,v
retrieving revision 1.4.2.1
retrieving revision 1.4.2.2
diff -C2 -d -r1.4.2.1 -r1.4.2.2
*** format.rb	14 Feb 2008 03:13:46 -0000	1.4.2.1
--- format.rb	14 Feb 2008 03:32:14 -0000	1.4.2.2
***************
*** 170,174 ****
      end
      result << left if left
!     return result.join("\n")
    end
  
--- 170,176 ----
      end
      result << left if left
!     result_string = result.join("\n")
!     result_string << "\n" unless result_string.empty?
!     return result_string
    end
  



From ngoto at dev.open-bio.org  Thu Feb 14 08:51:47 2008
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Thu, 14 Feb 2008 08:51:47 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/db/genbank genbank.rb,0.40,0.40.2.1
Message-ID: <200802140851.m1E8plsw023607@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/db/genbank
In directory dev.open-bio.org:/tmp/cvs-serv23587/lib/bio/db/genbank

Modified Files:
      Tag: BRANCH-biohackathon2008
	genbank.rb 
Log Message:
added new method Bio::GenBank#to_biosequence.


Index: genbank.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/genbank/genbank.rb,v
retrieving revision 0.40
retrieving revision 0.40.2.1
diff -C2 -d -r0.40 -r0.40.2.1
*** genbank.rb	5 Apr 2007 23:35:40 -0000	0.40
--- genbank.rb	14 Feb 2008 08:51:45 -0000	0.40.2.1
***************
*** 126,129 ****
--- 126,157 ----
    end
  
+   # converts Bio::GenBank to Bio::Sequence
+   # ---
+   # *Arguments*: 
+   # *Returns*:: Bio::Sequence object
+   def to_biosequence
+     sequence = Bio::Sequence.new(seq)
+     sequence.entry_id = self.entry_id
+ 
+     sequence.primary_accession = self.accession
+     sequence.secondary_accessions = self.accessions - [ self.accession ]
+ 
+     sequence.molecule_type = self.natype
+     sequence.division = self.division
+     sequence.topology = self.circular
+ 
+     sequence.sequence_version = self.version
+     seq.date_created = nil #????
+     sequence.date_modified = self.date
+ 
+     sequence.keywords = self.keywords
+     sequence.species = self.organism
+     sequence.classification = self.taxonomy
+     sequence.organnella = nil # not used
+     sequence.comments = self.comment
+     sequence.references = self.references
+     return sequence
+   end
+ 
  end # GenBank
  end # Bio



From ngoto at dev.open-bio.org  Fri Feb 15 02:18:24 2008
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Fri, 15 Feb 2008 02:18:24 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/sequence format.rb,1.4.2.2,1.4.2.3
Message-ID: <200802150218.m1F2IOnH025723@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/sequence
In directory dev.open-bio.org:/tmp/cvs-serv25703/lib/bio/sequence

Modified Files:
      Tag: BRANCH-biohackathon2008
	format.rb 
Log Message:
special character in regexp should be escaped


Index: format.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence/format.rb,v
retrieving revision 1.4.2.2
retrieving revision 1.4.2.3
diff -C2 -d -r1.4.2.2 -r1.4.2.3
*** format.rb	14 Feb 2008 03:32:14 -0000	1.4.2.2
--- format.rb	15 Feb 2008 02:18:21 -0000	1.4.2.3
***************
*** 157,161 ****
        line = nil
        width.downto(1) do |i|
!         if left[i..i] == ' ' or /[,;]/ =~ left[(i-1)..(i-1)]  then
            line = left[0..(i-1)].sub(/ +\z/, '')
            left = left[i..-1].sub(/\A +/, '')
--- 157,161 ----
        line = nil
        width.downto(1) do |i|
!         if left[i..i] == ' ' or /[\,\;]/ =~ left[(i-1)..(i-1)]  then
            line = left[0..(i-1)].sub(/ +\z/, '')
            left = left[i..-1].sub(/\A +/, '')



From ngoto at dev.open-bio.org  Fri Feb 15 03:23:25 2008
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Fri, 15 Feb 2008 03:23:25 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio sequence.rb,0.58.2.2,0.58.2.3
Message-ID: <200802150323.m1F3NP8b025922@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv25902/lib/bio

Modified Files:
      Tag: BRANCH-biohackathon2008
	sequence.rb 
Log Message:
In Bio::Sequence#method_missing, __send__ should be used instead of 
send. When method is not found, error message is modified if it is 
caused by method_missing.


Index: sequence.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence.rb,v
retrieving revision 0.58.2.2
retrieving revision 0.58.2.3
diff -C2 -d -r0.58.2.2 -r0.58.2.3
*** sequence.rb	14 Feb 2008 03:13:46 -0000	0.58.2.2
--- sequence.rb	15 Feb 2008 03:23:23 -0000	0.58.2.3
***************
*** 97,101 ****
    # http://www.rubycentral.com/book/ref_c_object.html#Object.method_missing
    def method_missing(sym, *args, &block) #:nodoc:
!     @seq.send(sym, *args, &block)
    end
    
--- 97,119 ----
    # http://www.rubycentral.com/book/ref_c_object.html#Object.method_missing
    def method_missing(sym, *args, &block) #:nodoc:
!     begin
!       @seq.__send__(sym, *args, &block)
!     rescue NoMethodError => evar
!       lineno = __LINE__ - 2
!       file = __FILE__
!       bt_here = [ "#{file}:#{lineno}:in \`__send__\'",
!                   "#{file}:#{lineno}:in \`method_missing\'"
!                 ]
!       if bt_here == evar.backtrace[0, 2] then
!         bt = evar.backtrace[2..-1]
!         evar = NoMethodError.new("undefined method \`#{sym.to_s}\' for #{self.inspect}")
!         evar.set_backtrace(bt)
!       end
!       #p lineno
!       #p file
!       #p bt_here
!       #p evar.backtrace
!       raise(evar)
!     end
    end
    



From ngoto at dev.open-bio.org  Fri Feb 15 03:33:53 2008
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Fri, 15 Feb 2008 03:33:53 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio sequence.rb,0.58.2.3,0.58.2.4
Message-ID: <200802150333.m1F3Xr5w025971@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv25951/lib/bio

Modified Files:
      Tag: BRANCH-biohackathon2008
	sequence.rb 
Log Message:
changed to use original exception class instead of NoMethodError 


Index: sequence.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence.rb,v
retrieving revision 0.58.2.3
retrieving revision 0.58.2.4
diff -C2 -d -r0.58.2.3 -r0.58.2.4
*** sequence.rb	15 Feb 2008 03:23:23 -0000	0.58.2.3
--- sequence.rb	15 Feb 2008 03:33:51 -0000	0.58.2.4
***************
*** 107,111 ****
        if bt_here == evar.backtrace[0, 2] then
          bt = evar.backtrace[2..-1]
!         evar = NoMethodError.new("undefined method \`#{sym.to_s}\' for #{self.inspect}")
          evar.set_backtrace(bt)
        end
--- 107,111 ----
        if bt_here == evar.backtrace[0, 2] then
          bt = evar.backtrace[2..-1]
!         evar = evar.class.new("undefined method \`#{sym.to_s}\' for #{self.inspect}")
          evar.set_backtrace(bt)
        end



From aerts at dev.open-bio.org  Fri Feb 15 04:49:39 2008
From: aerts at dev.open-bio.org (Jan Aerts)
Date: Fri, 15 Feb 2008 04:49:39 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/db/embl embl.rb,1.29,1.29.2.1
Message-ID: <200802150449.m1F4ndLY026633@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/db/embl
In directory dev.open-bio.org:/tmp/cvs-serv26608/db/embl

Modified Files:
      Tag: BRANCH-biohackathon2008
	embl.rb 
Log Message:
Added functionality to convert a Bio::EMBL object into a full-blown Bio::Sequence object that contains features, references and other additional 
information.


Index: embl.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/embl.rb,v
retrieving revision 1.29
retrieving revision 1.29.2.1
diff -C2 -d -r1.29 -r1.29.2.1
*** embl.rb	5 Apr 2007 23:35:40 -0000	1.29
--- embl.rb	15 Feb 2008 04:49:37 -0000	1.29.2.1
***************
*** 3,7 ****
  #
  # 
! # Copyright::   Copyright (C) 2001-2007 Mitsuteru C. Nakao <n at bioruby.org>
  # License::     The Ruby License
  #
--- 3,9 ----
  #
  # 
! # Copyright::   Copyright (C) 2001-2007
! #               Mitsuteru C. Nakao <n at bioruby.org>
! #               Jan Aerts <jan.aerts at bbsrc.ac.uk>
  # License::     The Ruby License
  #
***************
*** 121,124 ****
--- 123,130 ----
    alias molecule_type molecule
  
+   def topology
+     id_line('TOPOLOGY')
+   end
+   
    # returns DIVISION in the ID line.
    # * Bio::EMBL#division -> String
***************
*** 222,227 ****
    #
    # Bio::EMBLDB#ref
! 
! 
    ##
    # DR Line; defabases cross-regerence (>=0)
--- 228,233 ----
    #
    # Bio::EMBLDB#ref
!   
!   
    ##
    # DR Line; defabases cross-regerence (>=0)
***************
*** 356,366 ****
    # bb Line; (blanks) sequence data (>=1)
    def seq
!     Sequence::NA.new( fetch('').gsub(/ /,'').gsub(/\d+/,'') )
    end
    alias naseq seq
    alias ntseq seq
! 
    # // Line; termination line (end; 1/entry)
  
  
    ### private methods
--- 362,392 ----
    # bb Line; (blanks) sequence data (>=1)
    def seq
!     Bio::Sequence::NA.new( fetch('').gsub(/ /,'').gsub(/\d+/,'') )
    end
    alias naseq seq
    alias ntseq seq
!   
    # // Line; termination line (end; 1/entry)
  
+   def to_biosequence
+     bio_seq = Bio::Sequence.new(self.seq)
+     bio_seq.entry_id = self.entry_id
+     bio_seq.primary_accession = self.accessions[0]
+     bio_seq.secondary_accessions = self.accessions[1,-1]
+     bio_seq.molecule_type = self.molecule_type
+     bio_seq.definition = self.description
+     bio_seq.topology = self.topology
+     bio_seq.date_created = self.dt['created']
+     bio_seq.date_modified = self.dt['updated']
+     bio_seq.division = self.division
+     bio_seq.sequence_version = self.version
+     bio_seq.keywords = self.keywords
+     bio_seq.species = self.os(0)[0]['os'] + ' ' + self.os(0)[0]['name']
+     bio_seq.classification = self.oc
+     bio_seq.references = self.references
+     bio_seq.features = self.ft
+     
+     return bio_seq
+   end
  
    ### private methods
***************
*** 401,402 ****
--- 427,443 ----
  
  end # module Bio
+ 
+ if __FILE__ == $0
+   require '../../../bio'
+   require 'yaml'
+   
+   prefix = 'FT   '
+   indent = prefix + ' ' * 16
+   fwidth = 80 - indent.length
+   
+   parser = Bio::FlatFile.auto('/home/aertsj/LocalDocuments/hackathon/aj224122.embl')
+   parser.each do |entry|
+ #    entry.ref
+     puts entry.to_biosequence.output(:embl)
+   end
+ end
\ No newline at end of file



From aerts at dev.open-bio.org  Fri Feb 15 04:49:39 2008
From: aerts at dev.open-bio.org (Jan Aerts)
Date: Fri, 15 Feb 2008 04:49:39 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio sequence.rb,0.58.2.4,0.58.2.5
Message-ID: <200802150449.m1F4ndul026630@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv26608

Modified Files:
      Tag: BRANCH-biohackathon2008
	sequence.rb 
Log Message:
Added functionality to convert a Bio::EMBL object into a full-blown Bio::Sequence object that contains features, references and other additional 
information.


Index: sequence.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence.rb,v
retrieving revision 0.58.2.4
retrieving revision 0.58.2.5
diff -C2 -d -r0.58.2.4 -r0.58.2.5
*** sequence.rb	15 Feb 2008 03:33:51 -0000	0.58.2.4
--- sequence.rb	15 Feb 2008 04:49:37 -0000	0.58.2.5
***************
*** 13,16 ****
--- 13,17 ----
  #
  
+ require 'erb'
  require 'bio/sequence/compat'
  
***************
*** 73,76 ****
--- 74,79 ----
    include Format
  
+   attr_accessor :sequence_version, :topology, :molecule_type, :data_class, :division, :primary_accession, :secondary_accessions, :date_created, :date_modified, :species, :classification
+ 
    # Create a new Bio::Sequence object
    #
***************
*** 165,181 ****
    # ---
    # *Arguments*: 
!   # * (required) _style_: :fasta, :genbank, *or* :embl
    # *Returns*:: String object
!   def output(style)
!     case style
!     when :fasta
!       format_fasta
!     when :gff
!       format_gff
!     when :genbank
!       format_genbank
!     when :embl
!       format_embl
!     end
    end
  
--- 168,176 ----
    # ---
    # *Arguments*: 
!   # * (required) _format_: :fasta, :genbank, *or* :embl
    # *Returns*:: String object
!   def output(format = :fasta)
!     record_template = ERB.new(File.read(File.dirname(__FILE__) + "/db/#{format.to_s}/format.erb"))
!     record_template.result(binding)
    end
  
***************
*** 372,375 ****
--- 367,375 ----
    end
    
+   
+   def accessions
+     return [@primary_accession, @secondary_accessions].flatten
+   end
+   
  end # Sequence
  
***************
*** 380,510 ****
  if __FILE__ == $0
  
!   puts "== Test Bio::Sequence::NA.new"
!   p Bio::Sequence::NA.new('')
!   p na = Bio::Sequence::NA.new('atgcatgcATGCATGCAAAA')
!   p rna = Bio::Sequence::NA.new('augcaugcaugcaugcaaaa')
! 
!   puts "\n== Test Bio::Sequence::AA.new"
!   p Bio::Sequence::AA.new('')
!   p aa = Bio::Sequence::AA.new('ACDEFGHIKLMNPQRSTVWYU')
! 
!   puts "\n== Test Bio::Sequence#to_s"
!   p na.to_s
!   p aa.to_s
! 
!   puts "\n== Test Bio::Sequence#subseq(2,6)"
!   p na
!   p na.subseq(2,6)
! 
!   puts "\n== Test Bio::Sequence#[2,6]"
!   p na
!   p na[2,6]
! 
!   puts "\n== Test Bio::Sequence#to_fasta('hoge', 8)"
!   puts na.to_fasta('hoge', 8)
! 
!   puts "\n== Test Bio::Sequence#window_search(15)"
!   p na
!   na.window_search(15) {|x| p x}
! 
!   puts "\n== Test Bio::Sequence#total({'a'=>0.1,'t'=>0.2,'g'=>0.3,'c'=>0.4})"
!   p na.total({'a'=>0.1,'t'=>0.2,'g'=>0.3,'c'=>0.4})
! 
!   puts "\n== Test Bio::Sequence#composition"
!   p na
!   p na.composition
!   p rna
!   p rna.composition
! 
!   puts "\n== Test Bio::Sequence::NA#splicing('complement(join(1..5,16..20))')"
!   p na
!   p na.splicing("complement(join(1..5,16..20))")
!   p rna
!   p rna.splicing("complement(join(1..5,16..20))")
! 
!   puts "\n== Test Bio::Sequence::NA#complement"
!   p na.complement
!   p rna.complement
!   p Bio::Sequence::NA.new('tacgyrkmhdbvswn').complement
!   p Bio::Sequence::NA.new('uacgyrkmhdbvswn').complement
! 
!   puts "\n== Test Bio::Sequence::NA#translate"
!   p na
!   p na.translate
!   p rna
!   p rna.translate
! 
!   puts "\n== Test Bio::Sequence::NA#gc_percent"
!   p na.gc_percent
!   p rna.gc_percent
! 
!   puts "\n== Test Bio::Sequence::NA#illegal_bases"
!   p na.illegal_bases
!   p Bio::Sequence::NA.new('tacgyrkmhdbvswn').illegal_bases
!   p Bio::Sequence::NA.new('abcdefghijklmnopqrstuvwxyz-!%#$@').illegal_bases
! 
!   puts "\n== Test Bio::Sequence::NA#molecular_weight"
!   p na
!   p na.molecular_weight
!   p rna
!   p rna.molecular_weight
! 
!   puts "\n== Test Bio::Sequence::NA#to_re"
!   p Bio::Sequence::NA.new('atgcrymkdhvbswn')
!   p Bio::Sequence::NA.new('atgcrymkdhvbswn').to_re
!   p Bio::Sequence::NA.new('augcrymkdhvbswn')
!   p Bio::Sequence::NA.new('augcrymkdhvbswn').to_re
! 
!   puts "\n== Test Bio::Sequence::NA#names"
!   p na.names
! 
!   puts "\n== Test Bio::Sequence::NA#pikachu"
!   p na.pikachu
! 
!   puts "\n== Test Bio::Sequence::NA#randomize"
!   print "Orig  : "; p na
!   print "Rand  : "; p na.randomize
!   print "Rand  : "; p na.randomize
!   print "Rand  : "; p na.randomize.randomize
!   print "Block : "; na.randomize do |x| print x end; puts
! 
!   print "Orig  : "; p rna
!   print "Rand  : "; p rna.randomize
!   print "Rand  : "; p rna.randomize
!   print "Rand  : "; p rna.randomize.randomize
!   print "Block : "; rna.randomize do |x| print x end; puts
! 
!   puts "\n== Test Bio::Sequence::NA.randomize(counts)"
!   print "Count : "; p counts = {'a'=>10,'c'=>20,'g'=>30,'t'=>40}
!   print "Rand  : "; p Bio::Sequence::NA.randomize(counts)
!   print "Count : "; p counts = {'a'=>10,'c'=>20,'g'=>30,'u'=>40}
!   print "Rand  : "; p Bio::Sequence::NA.randomize(counts)
!   print "Block : "; Bio::Sequence::NA.randomize(counts) {|x| print x}; puts
! 
!   puts "\n== Test Bio::Sequence::AA#codes"
!   p aa
!   p aa.codes
! 
!   puts "\n== Test Bio::Sequence::AA#names"
!   p aa
!   p aa.names
! 
!   puts "\n== Test Bio::Sequence::AA#molecular_weight"
!   p aa.subseq(1,20)
!   p aa.subseq(1,20).molecular_weight
! 
!   puts "\n== Test Bio::Sequence::AA#randomize"
!   aaseq = 'MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA'
!   s = Bio::Sequence::AA.new(aaseq)
!   print "Orig  : "; p s
!   print "Rand  : "; p s.randomize
!   print "Rand  : "; p s.randomize
!   print "Rand  : "; p s.randomize.randomize
!   print "Block : "; s.randomize {|x| print x}; puts
  
!   puts "\n== Test Bio::Sequence::AA.randomize(counts)"
!   print "Count : "; p counts = s.composition
!   print "Rand  : "; puts Bio::Sequence::AA.randomize(counts)
!   print "Block : "; Bio::Sequence::AA.randomize(counts) {|x| print x}; puts
  
  end
--- 380,404 ----
  if __FILE__ == $0
  
!   require 'bio'
!   seq = Bio::Sequence.new('aattaaaacgccacgcaaggcgattctaggaaatcaaaacgacacgaaatgtggggtgggtgtttgggtaggaaagacagttgtcaacatcagggatttggattgaatcaaaaaaaaagtccttagatttcataaaagctaatcacgcctcaaaactggggcctatctcttcttttttgtcgcttcctgtcggtccttctctatttcttctccaacccctcatttttgaatatttacataacaaaccgttttactttctttggtcaaaattagacccaaaattctatattagtttaagatatgtggtctgtaatttattgttgtattgatataaaaattagttataagcgattatatttttatgctcaagtaactggtgttagttaactatattccaccacgataacctgattacataaaatatgattttaatcattttagtaaaccatatcgcacgttggatgattaattttaacggtttaataacacgtgattaaattatttttagaatgattatttacaaacggaaaagctatatgtgacacaataactcgtgcagtattgttagtttgaaaagtgtatttggtttcttatatttggcctcgattttcagtttatgtgctttttacaaagttttattttcgttatctgtttaacgcgacatttgttgtatggctttaccgatttgagaataaaatcatattacctttatgtagccatgtgtggtgtaatatataataatggtccttctacgaaaaaagcagatcacaattgaaataaagggtgaaatttggtgtcccttttcttcgtcgaaataacagaactaaataaaagaaagtgttatagtatattacgtccgaagaataatccatattcctgaaatacagtcaacatattatatatttagtactttatataaagttaggaattaaatcatatgttttatcgaccatattaagt!
 cacaactttatcataaattaatctgtaattagaattccaagttcgccaccgaatttcgtaacctaatctacatataatagataaaatatatatatgtagagtaattatgatatctatgtatgtagtcatggtatatgaattttgaaattggcaaggtaacattgacggatcgtaacccaacaaataatattaattacaaaatgggtgggcgggaatagtatacaactcataattccactcactttttgtattattaggatatgaaataagagtaatcaacatgcataataaagatgtataatttcttcatcttaaaaaacataactacatggtttaatacacaattttaccttttatcaaaaaagtatttcacaattcactcgcaaattacgaaatgatggctagtgcttcaactccaaatttcgaatattttaaatcacgatgtgtagaaccttttatttactggatactaatcactagtttattgagccaaccaattagttaaatagaacaatcaatattatagccagatattttttcctttaaaaatatttaaaagaggggccagaaaagaaccagagagggaggccatgagacattattatcactagtcaaaaacaacaaaccctccttttgctttttcatataaattattatattttattttgcaggtttcttctcttcttcttcttcttcttcttcttcttcctcttggctgctttctttcatcatccataaagtgaaagctaacgcatagagagagccatatcgtcccaaaaaaagcaaaagtccaaaaaaaaacaactccaaaacattctctcttagctctttactctttagtttctctctctctctctgcctttctctttgttgaagttcatggatgctacgaagtggactcaggtacgtaaaaagatatctctctgctatatctgtttgtttgtagcttctccccgactctcacgctctctctctctctctctctctc!
 tttgtgtatctctctactcacataaatatatacatgtgtgtgtatgcatgtttatatgtatgtatgaaac
cagtagtggttatacagatagtctatatagagatatcaatatgatgtgttttaatttagactttttatatatccgtttgaaacttccgaagttctcgaatggagttaaggaagttttgttctctacaagttcaatttttcttgtcattaattataaaactctgataactaatggataaaaaaggtatgctttgttagttaccttttgttcttggtgctcaggtcttaccatttttttcctaaattttaattagtctcctttctttaattaattttatgttaacgcactgacgatttaacgttaacaaaaaaacctagattctttttcttttcaatagagcataattattacttcaatttcatttatctcacactaaaccctaatcttggcgaaattccttttatatatataaatttaattaatttttccacaatcttggcggaattcaggactcggttttgcttgttattgttctctcttttaatttgacatggttagggaatacttaaagtatgtcttaattttatagggttttcaagaaatgataaacgtaaagccaatggagcaaatgatttctagcaccaacaacaacacaccgcaacaacaaccaacattcatcgccaccaacacaaggccaaacgccaccgcatccaatggtggctccggaggaaataccaacaacacggctacgatggaaactagaaaggcgaggccacaagagaaagtaaattgtccaagatgcaactcaacaaacacaaagttctgttattacaacaactacagtctcacgcaaccaagatacttctgcaaaggttgtcgaaggtattggaccgaaggtggctctcttcgtaacgtcccagtcggaggtagctcaagaaagaacaagagatcctctacacctttagcttcaccttctaatcccaaacttccagatctaaacccaccgattcttttctcaagccaaatccctaataagtcaaataaagatc!
 tcaacttgctatctttcccggtcatgcaagatcatcatcatcatggtatgtctcatttttttcatatgcccaagatagagaacaacaatacttcatcctcaatctatgcttcatcatctcctgtctcagctcttgagcttctaagatccaatggagtctcttcaagaggcatgaacacgttcttgcctggtcaaatgatggattcaaactcagtcctgtactcatctttagggtttccaacaatgcctgattacaaacagagtaataacaacctttcattctccattgatcatcatcaagggattggacataacaccatcaacagtaaccaaagagctcaagataacaatgatgacatgaatggagcaagtagggttttgttccctttttcagacatgaaagagctttcaagcacaacccaagagaagagtcatggtaataatacatattggaatgggatgttcagtaatacaggaggatcttcatggtgaaaaaaggttaaaaagagctcatgaactatcagctttcttctctttttctgtttttttctcctattttattatagtttttactttgatgatcttttgttttttctcacatggggaactttacttaaagttgtcagaacttagtttacagattgtctttttattccttctttctggttttccttttttcctttttttatcagtctttttaaaatatgtatttcataattgggtttgatcattcatatttattagtatcaaaatagagtctatgttcatgagggagtgttaaggggtgtgagggtagaagaataagtgaatacgggggcccg')
!   seq.entry_id = 'AJ224122'
!   seq.sequence_version = 3
!   seq.topology = 'linear'
!   seq.molecule_type = 'genomic DNA'
!   seq.data_class = 'STD'
!   seq.division = 'PLN'
!   seq.primary_accession = 'AJ224122'
!   seq.secondary_accessions = []
!   seq.date_created = '27-FEB-1998 (Rel. 54, Created)'
!   seq.date_modified = '14-NOV-2006 (Rel. 89, Last updated, Version 6)'
!   seq.definition = 'Arabidopsis thaliana DAG1 gene'
!   seq.keywords = ['BBFa gene', 'transcription factor']
!   seq.species = 'Arabidopsis thaliana (thale cress)'
!   seq.classification = ['Eukaryota', 'Viridiplantae', 'Streptophyta', 'Embryophyta', 'Tracheophyta',
!     'Spermatophyta', 'Magnoliophyta', 'eudicotyledons', 'core eudicotyledons', 'rosids',
!     'eurosids II', 'Brassicales', 'Brassicaceae', 'Arabidopsis']
  
! #  puts seq.output(:embl)
!   puts seq.output(:fasta)
  
  end



From ngoto at dev.open-bio.org  Fri Feb 15 05:29:52 2008
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Fri, 15 Feb 2008 05:29:52 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio sequence.rb,0.58.2.5,0.58.2.6
Message-ID: <200802150529.m1F5Tqn1026874@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv26854/lib/bio

Modified Files:
      Tag: BRANCH-biohackathon2008
	sequence.rb 
Log Message:
bugfix in Bio::Sequence.read: mistaken method name


Index: sequence.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence.rb,v
retrieving revision 0.58.2.5
retrieving revision 0.58.2.6
diff -C2 -d -r0.58.2.5 -r0.58.2.6
*** sequence.rb	15 Feb 2008 04:49:37 -0000	0.58.2.5
--- sequence.rb	15 Feb 2008 05:29:50 -0000	0.58.2.6
***************
*** 361,365 ****
        klass = format
      else
!       klass = Bio::FlatFile::AutoDetect.default.guess(str)
      end
      obj = klass.new(str)
--- 361,365 ----
        klass = format
      else
!       klass = Bio::FlatFile::AutoDetect.default.autodetect(str)
      end
      obj = klass.new(str)



From aerts at dev.open-bio.org  Mon Feb 18 15:43:29 2008
From: aerts at dev.open-bio.org (Jan Aerts)
Date: Mon, 18 Feb 2008 15:43:29 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/db/fasta - New directory
Message-ID: <200802181543.m1IFhTLc011233@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/db/fasta
In directory dev.open-bio.org:/tmp/cvs-serv11213/fasta

Log Message:
Directory /home/repository/bioruby/bioruby/lib/bio/db/fasta added to the repository
--> Using per-directory sticky tag `BRANCH-biohackathon2008'




From aerts at dev.open-bio.org  Mon Feb 18 15:44:41 2008
From: aerts at dev.open-bio.org (Jan Aerts)
Date: Mon, 18 Feb 2008 15:44:41 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio reference.rb,1.24,1.24.2.1
Message-ID: <200802181544.m1IFifJc011281@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv11261

Modified Files:
      Tag: BRANCH-biohackathon2008
	reference.rb 
Log Message:
Added export method to EMBL format.


Index: reference.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/reference.rb,v
retrieving revision 1.24
retrieving revision 1.24.2.1
diff -C2 -d -r1.24 -r1.24.2.1
*** reference.rb	5 Apr 2007 23:35:39 -0000	1.24
--- reference.rb	18 Feb 2008 15:44:39 -0000	1.24.2.1
***************
*** 2,8 ****
  # = bio/reference.rb - Journal reference classes
  #
! # Copyright::   Copyright (C) 2001, 2006
  #               Toshiaki Katayama <k at bioruby.org>,
! #               Ryan Raaum <ryan at raaum.org>
  # License::     The Ruby License
  #
--- 2,9 ----
  # = bio/reference.rb - Journal reference classes
  #
! # Copyright::   Copyright (C) 2001, 2006, 2008
  #               Toshiaki Katayama <k at bioruby.org>,
! #               Ryan Raaum <ryan at raaum.org>,
! #               Jan Aerts <jandot at bioruby.org>
  # License::     The Ruby License
  #
***************
*** 79,82 ****
--- 80,89 ----
      # Affiliations in an Array.
      attr_reader :affiliations
+     
+     # Sequence number in EMBL/GenBank records
+     attr_reader :embl_gb_record_number
+     
+     # Position in a sequence that this reference refers to
+     attr_reader :sequence_position
  
      # Create a new Bio::Reference object from a Hash of values. 
***************
*** 130,133 ****
--- 137,144 ----
        @url      = hash['url']
        @mesh     = hash['mesh']
+       @embl_gb_record_number = hash['embl_gb_record_number'] || nil
+       @sequence_position = hash['sequence_position'] || []
+       @comments = hash['comments'] || []
+       @xrefs    = hash['xrefs'] || []
        @affiliations = hash['affiliations']
        @authors = [] if @authors.empty?
***************
*** 171,174 ****
--- 182,187 ----
      def format(style = nil, option = nil)
        case style
+       when 'embl'
+         return embl
        when 'endnote'
          return endnote
***************
*** 246,249 ****
--- 259,298 ----
      end
  
+     # Returns reference formatted in the EMBL style.
+     #
+     #   # ref is a Bio::Reference object
+     #   puts ref.embl
+     #
+     #     RP   1-1859
+     #     RX   PUBMED; 1907511.
+     #     RA   Oxtoby E., Dunn M.A., Pancoro A., Hughes M.A.;
+     #     RT   "Nucleotide and derived amino acid sequence of the cyanogenic
+     #     RT   beta-glucosidase (linamarase) from white clover (Trifolium repens L.)";
+     #     RL   Plant Mol. Biol. 17(2):209-219(1991).
+     def embl
+       lines = Array.new
+       if ! @embl_gb_record_number.nil?
+         lines << "RN   [#{@embl_gb_record_number}]"
+       end
+       if @comments != []
+         @comments.each do |c|
+           lines << "RC   #{c}"
+         end
+       end
+       if @sequence_position != ''
+         lines << "RP   #{@sequence_position}"
+       end
+       if ! @xrefs.nil?
+         @xrefs.each do |x|
+           lines << "RX   #{x}"
+         end
+       end
+       lines << @authors.join(', ').wrap(80, 'RA   ') + ';' unless @authors.nil?
+       lines << (@title == '' ? 'RT   ;' : ('"' + @title + '"').wrap(80, 'RT   ') + ';')
+       lines << @journal.wrap(80, 'RL   ') unless @journal == ''
+       lines << "XX"
+       return lines.join("\n")
+     end
+ 
      # Returns reference formatted in the bibitem style
      #
***************
*** 542,546 ****
    #
    class References
! 
      # Array of Bio::Reference objects
      attr_accessor :references
--- 591,596 ----
    #
    class References
!     include Enumerable
!     
      # Array of Bio::Reference objects
      attr_accessor :references



From k at dev.open-bio.org  Tue Feb 19 03:36:54 2008
From: k at dev.open-bio.org (Katayama Toshiaki)
Date: Tue, 19 Feb 2008 03:36:54 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/io ncbirest.rb, NONE, 1.1 pubmed.rb,
	1.23, 1.24
Message-ID: <200802190336.m1J3as4O012327@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/io
In directory dev.open-bio.org:/tmp/cvs-serv12321

Modified Files:
	pubmed.rb 
Added Files:
	ncbirest.rb 
Log Message:
* NCBI E-Utilities (REST) functionality is separated to ncbirest.rb
  and pubmed.rb is changed to utilize the Bio::NCBI::REST class for
  esearch and efetch. You can now search and retrieve any database
  in any format that NCBI supports by E-Utilities through the
  Bio::NCBI::REST interface (currently, only esearch and efetch methods
  are implemented).


Index: pubmed.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/pubmed.rb,v
retrieving revision 1.23
retrieving revision 1.24
diff -C2 -d -r1.23 -r1.24
*** pubmed.rb	12 Dec 2007 13:53:26 -0000	1.23
--- pubmed.rb	19 Feb 2008 03:36:52 -0000	1.24
***************
*** 2,6 ****
  # = bio/io/pubmed.rb - NCBI Entrez/PubMed client module
  #
! # Copyright::  Copyright (C) 2001, 2007 Toshiaki Katayama <k at bioruby.org>
  # Copyright::  Copyright (C) 2006 Jan Aerts <jan.aerts at bbsrc.ac.uk>
  # License::    The Ruby License
--- 2,6 ----
  # = bio/io/pubmed.rb - NCBI Entrez/PubMed client module
  #
! # Copyright::  Copyright (C) 2001, 2007, 2008 Toshiaki Katayama <k at bioruby.org>
  # Copyright::  Copyright (C) 2006 Jan Aerts <jan.aerts at bbsrc.ac.uk>
  # License::    The Ruby License
***************
*** 9,12 ****
--- 9,13 ----
  #
  
+ require 'bio/io/ncbirest'
  require 'bio/command'
  require 'cgi' unless defined?(CGI)
***************
*** 69,95 ****
  #   medline = Bio::MEDLINE.new(manuscript)
  #  
! class PubMed
! 
!   # Run retrieval scripts on weekends or between 9 pm and 5 am Eastern Time
!   # weekdays for any series of more than 100 requests.
!   # -> Not implemented yet in BioRuby
! 
!   # Make no more than one request every 3 seconds.
!   NCBI_INTERVAL = 3
!   @@last_access = nil
! 
!   private
! 
!   def ncbi_access_wait(wait = NCBI_INTERVAL)
!     if @@last_access
!       duration = Time.now - @@last_access
!       if wait > duration
!         sleep wait - duration
!       end
!     end
!     @@last_access = Time.now
!   end
! 
!   public
  
    # Search the PubMed database by given keywords using E-Utils and returns 
--- 70,74 ----
  #   medline = Bio::MEDLINE.new(manuscript)
  #  
! class PubMed < Bio::NCBI::REST
  
    # Search the PubMed database by given keywords using E-Utils and returns 
***************
*** 100,136 ****
    # ---
    # *Arguments*:
!   # * _id_: query string (required)
!   # * _field_
!   # * _reldate_
!   # * _mindate_
!   # * _maxdate_
!   # * _datetype_
!   # * _retstart_
!   # * _retmax_ (default 100)
!   # * _retmode_
!   # * _rettype_
    # *Returns*:: array of PubMed IDs or a number of results
    def esearch(str, hash = {})
!     return nil if str.empty?
! 
!     serv = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"
!     opts = {
!       "retmax" => 100,
!       "tool"   => "bioruby",
!       "db"     => "pubmed",
!       "term"   => str
!     }
      opts.update(hash)
! 
!     ncbi_access_wait
! 
!     response, = Bio::Command.post_form(serv, opts)
!     result = response.body
!     if opts['rettype'] == 'count'
!       result = result.scan(/<Count>(.*?)<\/Count>/m).flatten.first.to_i
!     else
!       result = result.scan(/<Id>(.*?)<\/Id>/m).flatten
!     end
!     return result
    end
  
--- 79,98 ----
    # ---
    # *Arguments*:
!   # * _str_: query string (required)
!   # * _hash_: hash of E-Utils options
!   #   * _retmode_: "xml", "html", ...
!   #   * _rettype_: "medline", ...
!   #   * _retmax_: integer (default 100)
!   #   * _retstart_: integer
!   #   * _field_
!   #   * _reldate_
!   #   * _mindate_
!   #   * _maxdate_
!   #   * _datetype_
    # *Returns*:: array of PubMed IDs or a number of results
    def esearch(str, hash = {})
!     opts = { "db" => "pubmed" }
      opts.update(hash)
!     super(str, opts)
    end
  
***************
*** 142,168 ****
    # *Arguments*:
    # * _ids_: list of PubMed IDs (required)
    # *Returns*:: Array of MEDLINE formatted String
    def efetch(ids, hash = {})
!     return nil if ids.to_s.empty?
!     ids = ids.join(",") if ids === Array
! 
!     serv = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi"
!     opts = {
!       "tool"     => "bioruby",
!       "db"       => "pubmed",
!       "retmode"  => "text",
!       "rettype"  => "medline",
!       "id"       => ids,
!     }
      opts.update(hash)
! 
!     ncbi_access_wait
! 
!     response, = Bio::Command.post_form(serv, opts)
!     result = response.body
!     if opts["retmode"] == "text"
!       result = result.split(/\n\n+/)
!     end
!     return result
    end
  
--- 104,122 ----
    # *Arguments*:
    # * _ids_: list of PubMed IDs (required)
+   # * _hash_: hash of E-Utils options
+   #   * _retmode_: "xml", "html", ...
+   #   * _rettype_: "medline", ...
+   #   * _retmax_: integer (default 100)
+   #   * _retstart_: integer
+   #   * _field_
+   #   * _reldate_
+   #   * _mindate_
+   #   * _maxdate_
+   #   * _datetype_
    # *Returns*:: Array of MEDLINE formatted String
    def efetch(ids, hash = {})
!     opts = { "db" => "pubmed", "rettype"  => "medline" }
      opts.update(hash)
!     super(ids, opts)
    end
  

--- NEW FILE: ncbirest.rb ---
#
# = bio/io/ncbrest.rb - NCBI Entrez client module
#
# Copyright::  Copyright (C) 2008 Toshiaki Katayama <k at bioruby.org>
# License::    The Ruby License
#
# $Id: ncbirest.rb,v 1.1 2008/02/19 03:36:52 k Exp $
#

require 'bio/command'

module Bio

# == Description
#
# The Bio::NCBI::REST class provides REST client for the NCBI E-Utilities
#
# * Entrez utilities index:
#      http://www.ncbi.nlm.nih.gov/entrez/utils/utils_index.html
# * How to link:
#     http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helplinks.chapter.linkshelp
#
# == Usage
#
#  Bio::NCBI::REST.esearch("tardigrada", {"db"=>"nuccore", "rettype"=>"gb"})
#  Bio::NCBI::REST.esearch("yeast kinase", {"db"=>"nuccore", "rettype"=>"gb", "retmode"=>"xml", "retmax"=>5})
#  Bio::NCBI::REST.efetch("185041", {"db"=>"nuccore", "rettype"=>"gb"})
#  Bio::NCBI::REST.efetch("J00231", {"db"=>"nuccore", "rettype"=>"gb", "retmode"=>"xml"})
#  
class NCBI
class REST

  # Run retrieval scripts on weekends or between 9 pm and 5 am Eastern Time
  # weekdays for any series of more than 100 requests.
  # -> Not implemented yet in BioRuby

  # Make no more than one request every 3 seconds.
  NCBI_INTERVAL = 3
  @@last_access = nil

  private

  def ncbi_access_wait(wait = NCBI_INTERVAL)
    if @@last_access
      duration = Time.now - @@last_access
      if wait > duration
        sleep wait - duration
      end
    end
    @@last_access = Time.now
  end

  public

  # Search the NCBI database by given keywords using E-Utils and returns 
  # an array of entry IDs.
  # 
  # For information on the possible arguments, see
  #
  # * http://eutils.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html
  #
  # ---
  # *Arguments*:
  # * _str_: query string (required)
  # * _hash_: hash of E-Utils option {"db" => "nuccore", "rettype" => "gb"}
  #   * _db_: "nuccore", "pubmed", ...
  #   * _retmode_: "xml", "html", ...
  #   * _rettype_: "gb", "medline", "count", ...
  #   * _retmax_: integer (default 100)
  #   * _retstart_: integer
  #   * _field_
  #   * _reldate_
  #   * _mindate_
  #   * _maxdate_
  #   * _datetype_
  # *Returns*:: array of entry IDs or a number of results
  def esearch(str, hash = {})
    return nil if str.empty?

    serv = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"
    opts = {
      "retmax" => 100,
      "tool"   => "bioruby",
      "term"   => str
    }
    opts.update(hash)

    ncbi_access_wait

    response, = Bio::Command.post_form(serv, opts)
    result = response.body
    if opts['rettype'] == 'count'
      result = result.scan(/<Count>(.*?)<\/Count>/m).flatten.first.to_i
    else
      result = result.scan(/<Id>(.*?)<\/Id>/m).flatten
    end
    return result
  end

  # Retrieve a database entry by given ID and using E-Utils (efetch) and
  # returns an array of entry string. Multiple IDs can be supplied.
  # ---
  # *Arguments*:
  # * _ids_: list of NCBI entry IDs (required)
  # * _hash_: hash of E-Utils option {"db" => "nuccore", "rettype" => "gb"}
  #   * _db_: "nuccore", "pubmed", ...
  #   * _retmode_: "xml", "html", ...
  #   * _rettype_: "gb", "medline", "count",...
  #   * _retmax_: integer (default 100)
  #   * _retstart_: integer
  #   * _field_
  #   * _reldate_
  #   * _mindate_
  #   * _maxdate_
  #   * _datetype_
  # *Returns*:: Array of entry String
  def efetch(ids, hash = {})
    return nil if ids.to_s.empty?
    ids = ids.join(",") if ids === Array

    serv = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi"
    opts = {
      "tool"     => "bioruby",
      "retmode"  => "text",
      "id"       => ids,
    }
    opts.update(hash)

    ncbi_access_wait

    response, = Bio::Command.post_form(serv, opts)
    result = response.body
    if opts["retmode"] == "text"
      result = result.split(/\n\n+/)
    end
    return result
  end

  def self.esearch(*args)
    self.new.esearch(*args)
  end

  def self.efetch(*args)
    self.new.efetch(*args)
  end

end # REST
end # NCBI
end # Bio


if __FILE__ == $0

  gbopts = {"db"=>"nuccore", "rettype"=>"gb"}
  pmopts = {"db"=>"pubmed", "rettype"=>"medline"}
  count = {"rettype" => "count"}
  xml = {"retmode"=>"xml"}
  max = {"retmax"=>5}

  puts "=== class methods ==="

  puts "--- Search NCBI by E-Utils ---"

  puts Time.now
  puts "# count of 'tardigrada' in nuccore"
  puts Bio::NCBI::REST.esearch("tardigrada", gbopts.merge(count))

  puts Time.now
  puts "# max 5 'tardigrada' entries in nuccore"
  puts Bio::NCBI::REST.esearch("tardigrada", gbopts.merge(max))

  puts Time.now
  puts "# count of 'yeast kinase' in nuccore"
  puts Bio::NCBI::REST.esearch("yeast kinase", gbopts.merge(count))

  puts Time.now
  puts "# max 5 'yeast kinase' entries in nuccore (XML)"
  puts Bio::NCBI::REST.esearch("yeast kinase", gbopts.merge(xml).merge(max))

  puts Time.now
  puts "# count of 'genome&analysis|bioinformatics' in pubmed"
  puts Bio::NCBI::REST.esearch("(genome AND analysis) OR bioinformatics", pmopts.merge(count))

  puts Time.now
  puts "# max 5 'genome&analysis|bioinformatics' entries in pubmed (XML)"
  puts Bio::NCBI::REST.esearch("(genome AND analysis) OR bioinformatics", pmopts.merge(xml).merge(max))

  puts Time.now
  Bio::NCBI::REST.esearch("(genome AND analysis) OR bioinformatics", pmopts.merge(max)).each do |x|
    puts "# each of 5 'genome&analysis|bioinformatics' entries in pubmed"
    puts x
  end

  puts "--- Retrieve NCBI entry by E-Utils ---"

  puts Time.now
  puts "# '185041' entry in nuccore"
  puts Bio::NCBI::REST.efetch("185041", gbopts)

  puts Time.now
  puts "# 'J00231' entry in nuccore (XML)"
  puts Bio::NCBI::REST.efetch("J00231", gbopts.merge(xml))

  puts Time.now
  puts "# 16381885 entry in pubmed"
  puts Bio::NCBI::REST.efetch(16381885, pmopts)

  puts Time.now
  puts "# '16381885' entry in pubmed"
  puts Bio::NCBI::REST.efetch("16381885", pmopts)

  puts Time.now
  puts "# [10592173,14693808] entries in pubmed"
  puts Bio::NCBI::REST.efetch([10592173, 14693808], pmopts)

  puts Time.now
  puts "# [10592173,14693808] entries in pubmed (XML)"
  puts Bio::NCBI::REST.efetch([10592173, 14693808], pmopts.merge(xml))


  puts "=== instance methods ==="

  ncbi = Bio::NCBI::REST.new

  puts "--- Search NCBI by E-Utils ---"

  puts Time.now
  puts "# count of 'genome&analysis|bioinformatics' in pubmed"
  puts ncbi.esearch("(genome AND analysis) OR bioinformatics", pmopts.merge(count))

  puts Time.now
  puts "# max 5 'genome&analysis|bioinformatics' entries in pubmed"
  puts ncbi.esearch("(genome AND analysis) OR bioinformatics", pmopts.merge(max))

  puts Time.now
  ncbi.esearch("(genome AND analysis) OR bioinformatics", pmopts).each do |x|
    puts "# each 'genome&analysis|bioinformatics' entries in pubmed"
    puts x
  end

  puts "--- Retrieve NCBI entry by E-Utils ---"

  puts Time.now
  puts "# 16381885 entry in pubmed"
  puts ncbi.efetch(16381885, pmopts)

  puts Time.now
  puts "# [10592173,14693808] entries in pubmed"
  puts ncbi.efetch([10592173, 14693808], pmopts)

end



From k at dev.open-bio.org  Tue Feb 19 04:42:16 2008
From: k at dev.open-bio.org (Katayama Toshiaki)
Date: Tue, 19 Feb 2008 04:42:16 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/io hinv.rb,1.1,1.2
Message-ID: <200802190442.m1J4gGQZ012425@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/io
In directory dev.open-bio.org:/tmp/cvs-serv12421

Modified Files:
	hinv.rb 
Log Message:
* hit2acc fixed


Index: hinv.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/hinv.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** hinv.rb	9 Jan 2008 17:18:18 -0000	1.1
--- hinv.rb	19 Feb 2008 04:42:14 -0000	1.2
***************
*** 2,6 ****
  # = bio/io/hinv.rb - H-invDB web service (REST) client module
  #
! # Copyright::  Copyright (C) 2007 Toshiaki Katayama <k at bioruby.org>
  # License::    The Ruby License
  #
--- 2,6 ----
  # = bio/io/hinv.rb - H-invDB web service (REST) client module
  #
! # Copyright::  Copyright (C) 2008 Toshiaki Katayama <k at bioruby.org>
  # License::    The Ruby License
  #
***************
*** 137,141 ****
  
        def initialize
!         @url = BASE_URI + "hit2acc.php?hit="
        end
  
--- 137,141 ----
  
        def initialize
!         @url = BASE_URI + "hit2acc.php"
        end
  



From k at dev.open-bio.org  Tue Feb 19 04:49:37 2008
From: k at dev.open-bio.org (Katayama Toshiaki)
Date: Tue, 19 Feb 2008 04:49:37 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/io ncbirest.rb,1.1,1.2
Message-ID: <200802190449.m1J4nb9x012447@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/io
In directory dev.open-bio.org:/tmp/cvs-serv12443

Modified Files:
	ncbirest.rb 
Log Message:
* doc update


Index: ncbirest.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/ncbirest.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** ncbirest.rb	19 Feb 2008 03:36:52 -0000	1.1
--- ncbirest.rb	19 Feb 2008 04:49:35 -0000	1.2
***************
*** 1,4 ****
  #
! # = bio/io/ncbrest.rb - NCBI Entrez client module
  #
  # Copyright::  Copyright (C) 2008 Toshiaki Katayama <k at bioruby.org>
--- 1,4 ----
  #
! # = bio/io/ncbirest.rb - NCBI Entrez client module
  #
  # Copyright::  Copyright (C) 2008 Toshiaki Katayama <k at bioruby.org>
***************
*** 16,26 ****
  # The Bio::NCBI::REST class provides REST client for the NCBI E-Utilities
  #
! # * Entrez utilities index:
! #      http://www.ncbi.nlm.nih.gov/entrez/utils/utils_index.html
! # * How to link:
! #     http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helplinks.chapter.linkshelp
  #
  # == Usage
  #
  #  Bio::NCBI::REST.esearch("tardigrada", {"db"=>"nuccore", "rettype"=>"gb"})
  #  Bio::NCBI::REST.esearch("yeast kinase", {"db"=>"nuccore", "rettype"=>"gb", "retmode"=>"xml", "retmax"=>5})
--- 16,26 ----
  # The Bio::NCBI::REST class provides REST client for the NCBI E-Utilities
  #
! # Entrez utilities index:
! #
! # * http://www.ncbi.nlm.nih.gov/entrez/utils/utils_index.html
  #
  # == Usage
  #
+ #  Bio::NCBI::REST.esearch("tardigrada", {"db"=>"nuccore", "rettype"=>"count"})
  #  Bio::NCBI::REST.esearch("tardigrada", {"db"=>"nuccore", "rettype"=>"gb"})
  #  Bio::NCBI::REST.esearch("yeast kinase", {"db"=>"nuccore", "rettype"=>"gb", "retmode"=>"xml", "retmax"=>5})
***************
*** 64,69 ****
    # * _str_: query string (required)
    # * _hash_: hash of E-Utils option {"db" => "nuccore", "rettype" => "gb"}
!   #   * _db_: "nuccore", "pubmed", ...
!   #   * _retmode_: "xml", "html", ...
    #   * _rettype_: "gb", "medline", "count", ...
    #   * _retmax_: integer (default 100)
--- 64,69 ----
    # * _str_: query string (required)
    # * _hash_: hash of E-Utils option {"db" => "nuccore", "rettype" => "gb"}
!   #   * _db_: "nuccore", "nucleotide", "protein", "pubmed", ...
!   #   * _retmode_: "text", "xml", "html", ...
    #   * _rettype_: "gb", "medline", "count", ...
    #   * _retmax_: integer (default 100)
***************
*** 100,109 ****
    # Retrieve a database entry by given ID and using E-Utils (efetch) and
    # returns an array of entry string. Multiple IDs can be supplied.
    # ---
    # *Arguments*:
    # * _ids_: list of NCBI entry IDs (required)
    # * _hash_: hash of E-Utils option {"db" => "nuccore", "rettype" => "gb"}
!   #   * _db_: "nuccore", "pubmed", ...
!   #   * _retmode_: "xml", "html", ...
    #   * _rettype_: "gb", "medline", "count",...
    #   * _retmax_: integer (default 100)
--- 100,114 ----
    # Retrieve a database entry by given ID and using E-Utils (efetch) and
    # returns an array of entry string. Multiple IDs can be supplied.
+   #
+   # For information on the possible arguments, see
+   #
+   # * http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetch_help.html
+   #
    # ---
    # *Arguments*:
    # * _ids_: list of NCBI entry IDs (required)
    # * _hash_: hash of E-Utils option {"db" => "nuccore", "rettype" => "gb"}
!   #   * _db_: "nuccore", "nucleotide", "protein", "pubmed", ...
!   #   * _retmode_: "text", "xml", "html", ...
    #   * _rettype_: "gb", "medline", "count",...
    #   * _retmax_: integer (default 100)



From aerts at dev.open-bio.org  Wed Feb 20 09:56:24 2008
From: aerts at dev.open-bio.org (Jan Aerts)
Date: Wed, 20 Feb 2008 09:56:24 +0000
Subject: [BioRuby-cvs] bioruby ChangeLog,1.83,1.83.2.1
Message-ID: <200802200956.m1K9uOcm015785@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby
In directory dev.open-bio.org:/tmp/cvs-serv15755

Modified Files:
      Tag: BRANCH-biohackathon2008
	ChangeLog 
Log Message:
* Rewrote some of the code for converting EMBL files into Bio::Sequence.
* Added functionality to export Bio::Sequence to EMBL format.

Changes:
* renamed Sequence::Format#wrap and #fold to String#wrap and #fold (stored in bio.rb)
* lib/bio/db/common.rb:
    - rewrote def ref and def references
    - added to_biosequence
    - def references now returns an Array instead of a Bio::References object (tests changed accordingly)
* lib/bio/db/embl/embl.rb
    - def ft now returns Array instead of Bio::Features object (tests changed accordingly)
* lib/bio/db/embl/format.erb
* lib/bio/sequence/common.rb
    - added def format_embl


Index: ChangeLog
===================================================================
RCS file: /home/repository/bioruby/bioruby/ChangeLog,v
retrieving revision 1.83
retrieving revision 1.83.2.1
diff -C2 -d -r1.83 -r1.83.2.1
*** ChangeLog	12 Feb 2008 05:32:23 -0000	1.83
--- ChangeLog	20 Feb 2008 09:56:21 -0000	1.83.2.1
***************
*** 1,2 ****
--- 1,27 ----
+ 2008-02-20  Jan Aerts <jandot at bioruby.org>
+         * lib/bio/db/fasta.rb
+         * lib/bio/db/fasta/format.erb
+         * test/unit/bio/db/test_fasta.rb
+ 
+           Renamed #to_seq to #to_biosequence to reflect that same method in
+           embl.rb, genbank.rb and others.
+ 
+ 2008-02-20  Jan Aerts <jandot at bioruby.org>
+         * lib/bio.rb
+         * lib/bio/db/embl/common.rb
+         * lib/bio/db/embl/embl.rb
+         * lib/bio/db/embl/format.erb
+         * lib/bio/sequence/common.rb
+         * lib/bio/sequence/format.rb
+         * test/unit/bio/db/embl/test_embl_to_bioseq.rb
+ 
+         Fixed some bugs in importing EMBL files and added functionality to
+         export a Bio::Sequence to EMBL format.
+ 
+ 2008-02-18  Jan Aerts <jandot at bioruby.org>
+         * lib/bio/reference.rb
+ 
+           Added export method to EMBL format.
+ 
  2008-02-12  Naohisa Goto <ng at bioruby.org>
  



From aerts at dev.open-bio.org  Wed Feb 20 09:56:24 2008
From: aerts at dev.open-bio.org (Jan Aerts)
Date: Wed, 20 Feb 2008 09:56:24 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/db/embl format.erb, NONE,
	1.1.2.1 common.rb, 1.12, 1.12.2.1 embl.rb, 1.29.2.1, 1.29.2.2
Message-ID: <200802200956.m1K9uO6r015800@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/db/embl
In directory dev.open-bio.org:/tmp/cvs-serv15755/lib/bio/db/embl

Modified Files:
      Tag: BRANCH-biohackathon2008
	common.rb embl.rb 
Added Files:
      Tag: BRANCH-biohackathon2008
	format.erb 
Log Message:
* Rewrote some of the code for converting EMBL files into Bio::Sequence.
* Added functionality to export Bio::Sequence to EMBL format.

Changes:
* renamed Sequence::Format#wrap and #fold to String#wrap and #fold (stored in bio.rb)
* lib/bio/db/common.rb:
    - rewrote def ref and def references
    - added to_biosequence
    - def references now returns an Array instead of a Bio::References object (tests changed accordingly)
* lib/bio/db/embl/embl.rb
    - def ft now returns Array instead of Bio::Features object (tests changed accordingly)
* lib/bio/db/embl/format.erb
* lib/bio/sequence/common.rb
    - added def format_embl


--- NEW FILE: format.erb ---
ID   <%= entry_id %>; SV <%= sequence_version %>; <%= topology %>; <%= molecule_type %>; <%= data_class %>; <%= division %>; <%= seq.length %> BP.
XX
AC   <%= accessions.reject{|a| a.nil?}.join('; ') + ';' %>
XX
DT   <%= date_created %>
DT   <%= date_modified %>
XX
DE   <%= definition %>
XX
KW   <%= keywords.join('; ') %>.
XX
OS   <%= species %>
<%= classification.join('; ').wrap(80, 'OC   ') %>.
XX   
<%= references.collect{|ref| ref.format('embl')}.join("\n") %>
XX
FH   Key             Location/Qualifiers
FH
<%  prefix = 'FT   '
    indent = prefix + ' ' * 16
    fwidth = 80 - indent.length %><%= format_features(prefix, indent, fwidth) %>XX
SQ   Sequence <%= seq.length %> BP; <%= seq.composition.collect{|k,v| "#{v} #{k.upcase}"}.join('; ') + '; ' + (seq.gsub(/[ACTGactg]/, '').length.to_s ) + ' other;' %>
<%= seq.format_embl %>
//
Index: embl.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/embl.rb,v
retrieving revision 1.29.2.1
retrieving revision 1.29.2.2
diff -C2 -d -r1.29.2.1 -r1.29.2.2
*** embl.rb	15 Feb 2008 04:49:37 -0000	1.29.2.1
--- embl.rb	20 Feb 2008 09:56:22 -0000	1.29.2.2
***************
*** 123,126 ****
--- 123,130 ----
    alias molecule_type molecule
  
+   def data_class
+     id_line('DATA_CLASS')
+   end
+   
    def topology
      id_line('TOPOLOGY')
***************
*** 254,258 ****
      unless @data['FT']
        @data['FT'] = Array.new
-       ary = Array.new
        in_quote = false
        @orig['FT'].each_line do |line|
--- 258,261 ----
***************
*** 262,268 ****
          body = line[20,60].chomp # feature value (position, /qualifier=)
          if line =~ /^FT {3}(\S+)/
!           ary.push([ $1, body ]) # [ feature, position, /q="data", ... ]
          elsif body =~ /^ \// and not in_quote
!           ary.last.push(body)    # /q="data..., /q=data, /q
  
            if body =~ /=" / and body !~ /"$/
--- 265,271 ----
          body = line[20,60].chomp # feature value (position, /qualifier=)
          if line =~ /^FT {3}(\S+)/
!           @data['FT'].push([ $1, body ]) # [ feature, position, /q="data", ... ]
          elsif body =~ /^ \// and not in_quote
!           @data['FT'].last.push(body)    # /q="data..., /q=data, /q
  
            if body =~ /=" / and body !~ /"$/
***************
*** 271,275 ****
  
          else
!           ary.last.last << body # ...data..., ...data..."
  
            if body =~ /"$/
--- 274,278 ----
  
          else
!           @data['FT'].last.last << body # ...data..., ...data..."
  
            if body =~ /"$/
***************
*** 279,287 ****
        end
  
!       ary.map! do |subary|
          parse_qualifiers(subary)
        end
  
-       @data['FT'] = Features.new(ary)
      end
      if block_given?
--- 282,289 ----
        end
  
!       @data['FT'].map! do |subary|
          parse_qualifiers(subary)
        end
  
      end
      if block_given?
***************
*** 373,378 ****
      bio_seq.entry_id = self.entry_id
      bio_seq.primary_accession = self.accessions[0]
!     bio_seq.secondary_accessions = self.accessions[1,-1]
      bio_seq.molecule_type = self.molecule_type
      bio_seq.definition = self.description
      bio_seq.topology = self.topology
--- 375,381 ----
      bio_seq.entry_id = self.entry_id
      bio_seq.primary_accession = self.accessions[0]
!     bio_seq.secondary_accessions = self.accessions[1,-1] || []
      bio_seq.molecule_type = self.molecule_type
+     bio_seq.data_class = self.data_class
      bio_seq.definition = self.description
      bio_seq.topology = self.topology
***************
*** 382,386 ****
      bio_seq.sequence_version = self.version
      bio_seq.keywords = self.keywords
!     bio_seq.species = self.os(0)[0]['os'] + ' ' + self.os(0)[0]['name']
      bio_seq.classification = self.oc
      bio_seq.references = self.references
--- 385,389 ----
      bio_seq.sequence_version = self.version
      bio_seq.keywords = self.keywords
!     bio_seq.species = self.fetch('OS')
      bio_seq.classification = self.oc
      bio_seq.references = self.references
***************
*** 435,439 ****
    indent = prefix + ' ' * 16
    fwidth = 80 - indent.length
!   
    parser = Bio::FlatFile.auto('/home/aertsj/LocalDocuments/hackathon/aj224122.embl')
    parser.each do |entry|
--- 438,443 ----
    indent = prefix + ' ' * 16
    fwidth = 80 - indent.length
! 
! #  parser = Bio::FlatFile.auto('/home/aertsj/LocalDocuments/bioruby_biohackathon/bioruby/test/data/embl/AB090716.embl')
    parser = Bio::FlatFile.auto('/home/aertsj/LocalDocuments/hackathon/aj224122.embl')
    parser.each do |entry|

Index: common.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/common.rb,v
retrieving revision 1.12
retrieving revision 1.12.2.1
diff -C2 -d -r1.12 -r1.12.2.1
*** common.rb	5 Apr 2007 23:35:40 -0000	1.12
--- common.rb	20 Feb 2008 09:56:22 -0000	1.12.2.1
***************
*** 241,265 ****
    def ref
      unless @data['R']
!       ary = Array.new
!       get('R').split(/\nRN   /).each do |str|
!         raw = {'RN' => '', 'RC' => '', 'RP' => '', 'RX' => '', 
!                'RA' => '', 'RT' => '', 'RL' => '', 'RG' => ''}
!         str = 'RN   ' + str unless /^RN   / =~ str
!         str.split("\n").each do |line|
!           if /^(R[NPXARLCTG])   (.+)/ =~ line
!             raw[$1] += $2 + ' '
!           else
!             raise "Invalid format in R lines, \n[#{line}]\n"
            end
          end
!         raw.each_value {|v| 
!           v.strip! 
!           v.sub!(/^"/,'')
!           v.sub!(/;$/,'')
!           v.sub!(/"$/,'')
!         }
!         ary.push(raw)
        end
-       @data['R'] = ary
      end
      @data['R']
--- 241,305 ----
    def ref
      unless @data['R']
!       @data['R'] = Array.new
!       # Get the different references as 'blurbs' (the lines together)
!       reference_blurbs = get('R').split(/\nRN   /)
!       reference_blurbs.each_index do |i|
!         reference_blurbs[i] = 'RN   ' + reference_blurbs[i] unless reference_blurbs[i] =~ /^RN   /
!       end
!       
!       # For each reference, we'll first create a hash that looks like below.
!       # Suppose the input is:
!       #   RA   name1, name2, name3
!       #   RA   name4
!       #   RT   some part of the title that
!       #   RT   did not fit on one line
!       # Then the hash looks like:
!       #   h = {
!       #         'RA' => ["name1, name2, name3", "name4"],
!       #         'RT' => ["some part of the title that", "did not fit on one line"]
!       #       }
!       reference_blurbs.each do |rb|
!         line_based_data = Hash.new
!         rb.split(/\n/).each do |line|
!           key, value = line.scan(/^(R[A-Z])   "?(\[?.*[A-Za-z0-9]\]?)/)[0]
!           if line_based_data[key].nil?
!             line_based_data[key] = Array.new
            end
+           line_based_data[key].push(value)
          end
! 
!         # Now we have to sanitize the hash: the authors should be kept in an 
!         # array, the title should be 1 string, ... So the hash should look like:
!         #  h = {
!         #        'RA' => ["name1", "name2", "name3", "name4"],
!         #        'RT' => 'some part of the title that did not fit on one line'
!         #      }
!         line_based_data.keys.each do |key|
!           if ['RC', 'RP', 'RT', 'RL'].include?(key)
!             line_based_data[key] = line_based_data[key].join(' ')
!           elsif ['RA', 'RX'].include?(key)
!             sanitized_data = Array.new
!             line_based_data[key].each do |v|
!               sanitized_data.push(v.split(/\s*,\s*/))
!             end
!             line_based_data[key] = sanitized_data.flatten
!           elsif key == 'RN'
!             line_based_data[key] = line_based_data[key][0].sub(/^\[/,'').sub(/\]$/,'').to_i
!           end
!         end
!         
!         # And put it in @data. @data in the end looks like this:
!         #  data = [
!         #           {
!         #             'RA' => ["name1", "name2", "name3", "name4"],
!         #             'RT' => 'some part of the title that did not fit on one line'
!         #           },
!         #           {
!         #             'RA' => ["name1", "name2", "name3", "name4"],
!         #             'RT' => 'some part of the title that did not fit on one line'
!         #           }
!         #         ]
!         @data['R'].push(line_based_data)
        end
      end
      @data['R']
***************
*** 270,306 ****
    def references
      unless @data['references']
!       ary = self.ref.map {|ent|
!         hash = Hash.new('')
!         ent.each {|key, value|
            case key
            when 'RA'
!             hash['authors'] = value.split(/, /)
            when 'RT'
              hash['title'] = value
            when 'RL'
!             if value =~ /(.*) (\d+) \((\d+)\), (\d+-\d+) \((\d+)\)$/
!               hash['journal'] = $1
!               hash['volume']  = $2
!               hash['issue']   = $3
!               hash['pages']   = $4
!               hash['year']    = $5
!             else
!               hash['journal'] = value
!             end
            when 'RX'  # PUBMED, MEDLINE
!             value.split('.').each {|item|
                tag, xref = item.split(/; /).map {|i| i.strip }
                hash[ tag.downcase ]  = xref
              }
            end
!         }
!         Reference.new(hash)
!       }
!       @data['references'] = References.new(ary)
      end
      @data['references']
    end
  
- 
    # returns contents in the DR line.
    # * Bio::EMBLDB::Common#dr  -> [ <Database cross-reference Hash>* ]
--- 310,345 ----
    def references
      unless @data['references']
!       @data['references'] = Array.new
!       self.ref.each do |ref|
!         hash = Hash.new
!         ref.each do |key, value|
            case key
+           when 'RN'
+             hash['embl_gb_record_number'] = value
+           when 'RC'
+             hash['comments'] = value
+           when 'RX'
+             hash['xrefs'] = value
+           when 'RP'
+             hash['sequence_position'] = value
            when 'RA'
!             hash['authors'] = value
            when 'RT'
              hash['title'] = value
            when 'RL'
!             hash['journal'] = value
            when 'RX'  # PUBMED, MEDLINE
!             value.each {|item|
                tag, xref = item.split(/; /).map {|i| i.strip }
                hash[ tag.downcase ]  = xref
              }
            end
!         end
!         @data['references'].push(Reference.new(hash))
!       end
      end
      @data['references']
    end
  
    # returns contents in the DR line.
    # * Bio::EMBLDB::Common#dr  -> [ <Database cross-reference Hash>* ]



From aerts at dev.open-bio.org  Wed Feb 20 09:56:24 2008
From: aerts at dev.open-bio.org (Jan Aerts)
Date: Wed, 20 Feb 2008 09:56:24 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio sequence.rb,0.58.2.6,0.58.2.7
Message-ID: <200802200956.m1K9uO8C015795@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv15755/lib/bio

Modified Files:
      Tag: BRANCH-biohackathon2008
	sequence.rb 
Log Message:
* Rewrote some of the code for converting EMBL files into Bio::Sequence.
* Added functionality to export Bio::Sequence to EMBL format.

Changes:
* renamed Sequence::Format#wrap and #fold to String#wrap and #fold (stored in bio.rb)
* lib/bio/db/common.rb:
    - rewrote def ref and def references
    - added to_biosequence
    - def references now returns an Array instead of a Bio::References object (tests changed accordingly)
* lib/bio/db/embl/embl.rb
    - def ft now returns Array instead of Bio::Features object (tests changed accordingly)
* lib/bio/db/embl/format.erb
* lib/bio/sequence/common.rb
    - added def format_embl


Index: sequence.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence.rb,v
retrieving revision 0.58.2.6
retrieving revision 0.58.2.7
diff -C2 -d -r0.58.2.6 -r0.58.2.7
*** sequence.rb	15 Feb 2008 05:29:50 -0000	0.58.2.6
--- sequence.rb	20 Feb 2008 09:56:22 -0000	0.58.2.7
***************
*** 371,375 ****
      return [@primary_accession, @secondary_accessions].flatten
    end
!   
  end # Sequence
  
--- 371,375 ----
      return [@primary_accession, @secondary_accessions].flatten
    end
! 
  end # Sequence
  



From aerts at dev.open-bio.org  Wed Feb 20 09:56:24 2008
From: aerts at dev.open-bio.org (Jan Aerts)
Date: Wed, 20 Feb 2008 09:56:24 +0000
Subject: [BioRuby-cvs] bioruby/lib bio.rb,1.89,1.89.2.1
Message-ID: <200802200956.m1K9uOdN015790@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib
In directory dev.open-bio.org:/tmp/cvs-serv15755/lib

Modified Files:
      Tag: BRANCH-biohackathon2008
	bio.rb 
Log Message:
* Rewrote some of the code for converting EMBL files into Bio::Sequence.
* Added functionality to export Bio::Sequence to EMBL format.

Changes:
* renamed Sequence::Format#wrap and #fold to String#wrap and #fold (stored in bio.rb)
* lib/bio/db/common.rb:
    - rewrote def ref and def references
    - added to_biosequence
    - def references now returns an Array instead of a Bio::References object (tests changed accordingly)
* lib/bio/db/embl/embl.rb
    - def ft now returns Array instead of Bio::Features object (tests changed accordingly)
* lib/bio/db/embl/format.erb
* lib/bio/sequence/common.rb
    - added def format_embl


Index: bio.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio.rb,v
retrieving revision 1.89
retrieving revision 1.89.2.1
diff -C2 -d -r1.89 -r1.89.2.1
*** bio.rb	9 Jan 2008 17:18:17 -0000	1.89
--- bio.rb	20 Feb 2008 09:56:22 -0000	1.89.2.1
***************
*** 278,279 ****
--- 278,310 ----
  end
  
+ class String
+   def fold(width = 80)
+     self.gsub(Regexp.new("(.{1,#{width}})"), "\\1\n")
+   end
+   
+   def wrap(width = 80, prefix = '')
+     actual_width = width - prefix.length
+     result = []
+     left = self.dup
+     while left and left.length > actual_width
+       line = nil
+       actual_width.downto(1) do |i|
+         if left[i..i] == ' ' or /[,;]/ =~ left[(i-1)..(i-1)]  then
+           line = left[0..(i-1)].sub(/ +\z/, '')
+           left = left[i..-1].sub(/\A +/, '')
+           break
+         end
+       end
+       if line.nil? then
+         line = left[0..(actual_width-1)]
+         left = left[actual_width..-1]
+       end
+       result << line
+     end
+     result << left if left
+     result_string = result.join("\n#{prefix}")
+     result_string = prefix + result_string unless result_string.empty?
+ #    result_string << "\n" unless result_string.empty?
+     return result_string
+   end
+ end
\ No newline at end of file



From aerts at dev.open-bio.org  Wed Feb 20 09:56:24 2008
From: aerts at dev.open-bio.org (Jan Aerts)
Date: Wed, 20 Feb 2008 09:56:24 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/sequence common.rb, 1.6,
	1.6.2.1 format.rb, 1.4.2.3, 1.4.2.4
Message-ID: <200802200956.m1K9uOhl015806@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/sequence
In directory dev.open-bio.org:/tmp/cvs-serv15755/lib/bio/sequence

Modified Files:
      Tag: BRANCH-biohackathon2008
	common.rb format.rb 
Log Message:
* Rewrote some of the code for converting EMBL files into Bio::Sequence.
* Added functionality to export Bio::Sequence to EMBL format.

Changes:
* renamed Sequence::Format#wrap and #fold to String#wrap and #fold (stored in bio.rb)
* lib/bio/db/common.rb:
    - rewrote def ref and def references
    - added to_biosequence
    - def references now returns an Array instead of a Bio::References object (tests changed accordingly)
* lib/bio/db/embl/embl.rb
    - def ft now returns Array instead of Bio::Features object (tests changed accordingly)
* lib/bio/db/embl/format.erb
* lib/bio/sequence/common.rb
    - added def format_embl


Index: format.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence/format.rb,v
retrieving revision 1.4.2.3
retrieving revision 1.4.2.4
diff -C2 -d -r1.4.2.3 -r1.4.2.4
*** format.rb	15 Feb 2008 02:18:21 -0000	1.4.2.3
--- format.rb	20 Feb 2008 09:56:22 -0000	1.4.2.4
***************
*** 31,106 ****
  #   puts s.output(:embl)
  module Format
- 
-   # INTERNAL USE ONLY, YOU SHOULD NOT CALL THIS METHOD. (And in any
-   # case, it would be difficult to successfully call this method outside
-   # its expected context).
-   #
-   # Output the FASTA format string of the sequence.  
-   #
-   # UNFORTUNATLY, the current implementation of Bio::Sequence is incapable of 
-   # using either the header or width arguments.  So something needs to be
-   # changed...
-   #
-   # Currently, this method is used in Bio::Sequence#output like so,
-   #
-   #   s = Bio::Sequence.new('atgc')
-   #   puts s.output(:fasta)                   #=> "> \natgc\n"
-   # ---
-   # *Arguments*:
-   # * (optional) _header_: String (default nil)
-   # * (optional) _width_: Fixnum (default nil)
-   # *Returns*:: String object
-   def format_fasta(header = nil, width = nil)
-     header ||= "#{@entry_id} #{@definition}"
- 
-     ">#{header}\n" +
-     if width
-       @seq.to_s.gsub(Regexp.new(".{1,#{width}}"), "\\0\n")
-     else
-       @seq.to_s + "\n"
-     end
-   end
- 
-   # Not yet implemented :)
-   # Remove the nodoc command after implementation!
-   # ---
-   # *Returns*:: String object
-   def format_gff #:nodoc:
-     raise NotImplementedError
-   end
- 
-   # INTERNAL USE ONLY, YOU SHOULD NOT CALL THIS METHOD. (And in any
-   # case, it would be difficult to successfully call this method outside
-   # its expected context).
-   #
-   # Output the Genbank format string of the sequence.  
-   # Used in Bio::Sequence#output.
-   # ---
-   # *Returns*:: String object
-   def format_genbank
-     prefix = ' ' * 5
-     indent = prefix + ' ' * 16
-     fwidth = 79 - indent.length
- 
-     format_features(prefix, indent, fwidth)
-   end
- 
-   # INTERNAL USE ONLY, YOU SHOULD NOT CALL THIS METHOD. (And in any
-   # case, it would be difficult to successfully call this method outside
-   # its expected context).
-   #
-   # Output the EMBL format string of the sequence.  
-   # Used in Bio::Sequence#output.
-   # ---
-   # *Returns*:: String object
-   def format_embl
-     prefix = 'FT   '
-     indent = prefix + ' ' * 16
-     fwidth = 80 - indent.length
- 
-     format_features(prefix, indent, fwidth)
-   end
- 
- 
    private
  
--- 31,34 ----
***************
*** 114,123 ****
  
        head = ''
!       wrap(position, width).each_line do |line|
          result << head << line
          head = indent
        end
  
!       result << format_qualifiers(feature.qualifiers, width)
      end
      return result
--- 42,51 ----
  
        head = ''
!       (position).wrap(width).each_line do |line|
          result << head << line
          head = indent
        end
  
!       result << format_qualifiers(feature.qualifiers, indent, width)
      end
      return result
***************
*** 130,136 ****
  
        if v == true
!         lines = wrap('/' + q, width)
        elsif q == 'translation'
!         lines = fold('/' + q + '=' + v, width)
        else
          if v[/\D/]
--- 58,64 ----
  
        if v == true
!         lines =('/' + q).wrap(width)
        elsif q == 'translation'
!         lines = ('/' + q + '="' + v + '"').fold(width)
        else
          if v[/\D/]
***************
*** 139,143 ****
            v = '"' + v + '"'
          end
!         lines = wrap('/' + q + '=' + v, width)
        end
  
--- 67,71 ----
            v = '"' + v + '"'
          end
!         lines = ('/' + q + '=' + v).wrap(width)
        end
  
***************
*** 147,177 ****
    end
  
-   def fold(str, width)
-     str.gsub(Regexp.new("(.{1,#{width}})"), "\\1\n")
-   end
- 
-   def wrap(str, width)
-     result = []
-     left = str.dup
-     while left and left.length > width
-       line = nil
-       width.downto(1) do |i|
-         if left[i..i] == ' ' or /[\,\;]/ =~ left[(i-1)..(i-1)]  then
-           line = left[0..(i-1)].sub(/ +\z/, '')
-           left = left[i..-1].sub(/\A +/, '')
-           break
-         end
-       end
-       if line.nil? then
-         line = left[0..(width-1)]
-         left = left[width..-1]
-       end
-       result << line
-     end
-     result << left if left
-     result_string = result.join("\n")
-     result_string << "\n" unless result_string.empty?
-     return result_string
-   end
  
  end # Format
--- 75,78 ----

Index: common.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence/common.rb,v
retrieving revision 1.6
retrieving revision 1.6.2.1
diff -C2 -d -r1.6 -r1.6.2.1
*** common.rb	27 Dec 2007 17:36:02 -0000	1.6
--- common.rb	20 Feb 2008 09:56:22 -0000	1.6.2.1
***************
*** 38,42 ****
  #   puts dna.randomize
  module Common
! 
    # Return sequence as 
    # String[http://corelib.rubyonrails.org/classes/String.html].
--- 38,42 ----
  #   puts dna.randomize
  module Common
!   
    # Return sequence as 
    # String[http://corelib.rubyonrails.org/classes/String.html].
***************
*** 66,69 ****
--- 66,86 ----
      self.class.new(self)
    end
+   
+   def format_embl
+     output_lines = Array.new
+     counter = 0
+     remainder = self.window_search(60,60) do |subseq|
+       counter += 60
+       subseq.gsub!(/(.{10})/, '\1 ')
+       output_lines.push(' '*5 + subseq + counter.to_s.rjust(9))
+     end
+     counter += remainder.length
+     remainder = (remainder.to_s + ' '*(60-remainder.length))
+     remainder.gsub!(/(.{10})/, '\1 ')
+     output_lines.push(' '*5 + remainder + counter.to_s.rjust(9))
+     return output_lines.join("\n")
+   end
+ 
+ 
  
    # Normalize the current sequence, removing all whitespace and 



From aerts at dev.open-bio.org  Wed Feb 20 09:56:24 2008
From: aerts at dev.open-bio.org (Jan Aerts)
Date: Wed, 20 Feb 2008 09:56:24 +0000
Subject: [BioRuby-cvs] bioruby/test/unit/bio/db/embl test_embl_to_bioseq.rb,
	NONE, 1.1.2.1 test_embl.rb, 1.5, 1.5.2.1 test_embl_rel89.rb,
	1.2, 1.2.2.1
Message-ID: <200802200956.m1K9uOKd015812@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/unit/bio/db/embl
In directory dev.open-bio.org:/tmp/cvs-serv15755/test/unit/bio/db/embl

Modified Files:
      Tag: BRANCH-biohackathon2008
	test_embl.rb test_embl_rel89.rb 
Added Files:
      Tag: BRANCH-biohackathon2008
	test_embl_to_bioseq.rb 
Log Message:
* Rewrote some of the code for converting EMBL files into Bio::Sequence.
* Added functionality to export Bio::Sequence to EMBL format.

Changes:
* renamed Sequence::Format#wrap and #fold to String#wrap and #fold (stored in bio.rb)
* lib/bio/db/common.rb:
    - rewrote def ref and def references
    - added to_biosequence
    - def references now returns an Array instead of a Bio::References object (tests changed accordingly)
* lib/bio/db/embl/embl.rb
    - def ft now returns Array instead of Bio::Features object (tests changed accordingly)
* lib/bio/db/embl/format.erb
* lib/bio/sequence/common.rb
    - added def format_embl


--- NEW FILE: test_embl_to_bioseq.rb ---
#
# test/unit/bio/db/embl/test_embl.rb - Unit test for Bio::EMBL
#
# Copyright::  Copyright (C) 2005, 2008
#                 Mitsuteru Nakao <n at bioruby.org>
#                 Jan Aerts <jan.aerts at bbsrc.ac.uk>
# License::    The Ruby License
#
#  $Id: test_embl_to_bioseq.rb,v 1.1.2.1 2008/02/20 09:56:22 aerts Exp $
#

require 'pathname'
libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
$:.unshift(libpath) unless $:.include?(libpath)

require 'test/unit'
require 'bio'
require 'bio/db/embl/embl'

module Bio
  class TestEMBLToBioSequence < Test::Unit::TestCase
    
    def setup
      bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
      input = File.open(File.join(bioruby_root, 'test', 'data', 'embl', 'AB090716.embl.rel89')).read
      embl_object = Bio::EMBL.new(input)
      embl_object.instance_eval { @data['OS'] = "Haplochromis sp. 'muzu rukwa'" }
      @bio_seq = embl_object.to_biosequence
    end

    def test_entry_id
      assert_equal('AB090716', @bio_seq.entry_id)
    end
    
    def test_primary_accession
      assert_equal('AB090716', @bio_seq.primary_accession)
    end
    
    def test_secondary_accessions
      assert_equal([], @bio_seq.secondary_accessions)
    end
    
    def test_molecule_type
      assert_equal('genomic DNA', @bio_seq.molecule_type)
    end
    
    def test_definition
      assert_equal("Haplochromis sp. 'muzu, rukwa' LWS gene for long wavelength-sensitive opsin, partial cds, specimen_voucher:specimen No. HT-9361.", @bio_seq.definition)
    end

    def test_topology
      assert_equal('linear', @bio_seq.topology)
    end
    
    def test_dates
      assert_equal('25-OCT-2002 (Rel. 73, Created)', @bio_seq.date_created)
      assert_equal('14-NOV-2006 (Rel. 89, Last updated, Version 3)', @bio_seq.date_modified)
    end
    
    def test_division
      assert_equal('VRT', @bio_seq.division)
    end
    
    def test_sequence_version
      assert_equal(1, @bio_seq.sequence_version)
    end
    
    def test_keywords
      assert_equal([], @bio_seq.keywords)
    end
    
    def test_species
      assert_equal("Haplochromis sp. 'muzu, rukwa'", @bio_seq.species)
    end
    
    def test_classification
      assert_equal(['Eukaryota','Metazoa','Chordata','Craniata','Vertebrata','Euteleostomi','Actinopterygii','Neopterygii','Teleostei','Euteleostei','Neoteleostei','Acanthomorpha','Acanthopterygii','Percomorpha','Perciformes','Labroidei','Cichlidae','African cichlids','Pseudocrenilabrinae','Haplochromini','Haplochromis'], @bio_seq.classification)
      

    end

    def test_references
      assert_equal(2, @bio_seq.references.length)
      assert_equal(Bio::Reference, @bio_seq.references[0].class)
    end
    
    def test_features
      assert_equal(3, @bio_seq.features.length)
      assert_equal(Bio::Feature, @bio_seq.features[0].class)
    end
    
  end

  # To really test the Bio::EMBL to Bio::Sequence conversion, we need to test if
  # that Bio::Sequence can be made into a valid Bio::EMBL again.
  class TestEMBLToBioSequenceRoundTrip < Test::Unit::TestCase
    def setup
      bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
      input = File.open(File.join(bioruby_root, 'test', 'data', 'embl', 'AB090716.embl.rel89')).read
      embl_object_1 = Bio::EMBL.new(input)
      embl_object_1.instance_eval { @data['OS'] = "Haplochromis sp. 'muzu rukwa'" }
      @bio_seq_1 = embl_object_1.to_biosequence
      embl_object_2 = Bio::EMBL.new(@bio_seq_1.output(:embl))
      @bio_seq_2 = embl_object_2.to_biosequence
    end
    
    def test_entry_id
      assert_equal('AB090716', @bio_seq_2.entry_id)
    end
    
    def test_primary_accession
      assert_equal('AB090716', @bio_seq_2.primary_accession)
    end
    
    def test_secondary_accessions
      assert_equal([], @bio_seq_2.secondary_accessions)
    end
    
    def test_molecule_type
      assert_equal('genomic DNA', @bio_seq_2.molecule_type)
    end
    
    def test_definition
      assert_equal("Haplochromis sp. 'muzu, rukwa' LWS gene for long wavelength-sensitive opsin, partial cds, specimen_voucher:specimen No. HT-9361.", @bio_seq_2.definition)
    end

    def test_topology
      assert_equal('linear', @bio_seq_2.topology)
    end
    
    def test_dates
      assert_equal('25-OCT-2002 (Rel. 73, Created)', @bio_seq_2.date_created)
      assert_equal('14-NOV-2006 (Rel. 89, Last updated, Version 3)', @bio_seq_2.date_modified)
    end
    
    def test_division
      assert_equal('VRT', @bio_seq_2.division)
    end
    
    def test_sequence_version
      assert_equal(1, @bio_seq_2.sequence_version)
    end
    
    def test_keywords
      assert_equal([], @bio_seq_2.keywords)
    end
    
    def test_species
      assert_equal("Haplochromis sp. 'muzu, rukwa'", @bio_seq_2.species)
    end
    
    def test_classification
      assert_equal(['Eukaryota','Metazoa','Chordata','Craniata','Vertebrata','Euteleostomi','Actinopterygii','Neopterygii','Teleostei','Euteleostei','Neoteleostei','Acanthomorpha','Acanthopterygii','Percomorpha','Perciformes','Labroidei','Cichlidae','African cichlids','Pseudocrenilabrinae','Haplochromini','Haplochromis'], @bio_seq_2.classification)
      

    end

    def test_references
      assert_equal(2, @bio_seq_2.references.length)
      assert_equal(Bio::Reference, @bio_seq_2.references[0].class)
    end
    
    def test_features a
      assert_equal(3, @bio_seq_2.features.length)
      assert_equal(Bio::Feature, @bio_seq_2.features[0].class)
    end
  end
end


Index: test_embl_rel89.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/embl/test_embl_rel89.rb,v
retrieving revision 1.2
retrieving revision 1.2.2.1
diff -C2 -d -r1.2 -r1.2.2.1
*** test_embl_rel89.rb	5 Apr 2007 23:35:43 -0000	1.2
--- test_embl_rel89.rb	20 Feb 2008 09:56:22 -0000	1.2.2.1
***************
*** 156,160 ****
      # Bio::EMBLDB::COMMON#references
      def test_references 
!       assert_equal(Bio::References, @obj.references.class)
      end
  
--- 156,160 ----
      # Bio::EMBLDB::COMMON#references
      def test_references 
!       assert_equal(Array, @obj.references.class)
      end
  
***************
*** 169,173 ****
  
      def test_ft
!       assert_equal(Bio::Features, @obj.ft.class)
      end
  
--- 169,173 ----
  
      def test_ft
!       assert_equal(Array, @obj.ft.class)
      end
  
***************
*** 179,183 ****
  
      def test_ft_accessor
!       assert_equal('CDS', @obj.ft.features[1].feature)
      end
  
--- 179,183 ----
  
      def test_ft_accessor
!       assert_equal('CDS', @obj.ft[1].feature)
      end
  

Index: test_embl.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/embl/test_embl.rb,v
retrieving revision 1.5
retrieving revision 1.5.2.1
diff -C2 -d -r1.5 -r1.5.2.1
*** test_embl.rb	5 Apr 2007 23:35:43 -0000	1.5
--- test_embl.rb	20 Feb 2008 09:56:22 -0000	1.5.2.1
***************
*** 151,155 ****
      # Bio::EMBLDB::COMMON#references
      def test_references 
!       assert_equal(Bio::References, @obj.references.class)
      end
  
--- 151,155 ----
      # Bio::EMBLDB::COMMON#references
      def test_references 
!       assert_equal(Array, @obj.references.class)
      end
  
***************
*** 164,168 ****
  
      def test_ft
!       assert_equal(Bio::Features, @obj.ft.class)
      end
  
--- 164,168 ----
  
      def test_ft
!       assert_equal(Array, @obj.ft.class)
      end
  
***************
*** 174,178 ****
  
      def test_ft_accessor
!       assert_equal('CDS', @obj.ft.features[1].feature)
      end
  
--- 174,178 ----
  
      def test_ft_accessor
!       assert_equal('CDS', @obj.ft[1].feature)
      end
  



From aerts at dev.open-bio.org  Wed Feb 20 13:54:21 2008
From: aerts at dev.open-bio.org (Jan Aerts)
Date: Wed, 20 Feb 2008 13:54:21 +0000
Subject: [BioRuby-cvs] bioruby/lib bio.rb,1.89.2.1,1.89.2.2
Message-ID: <200802201354.m1KDsL5F016175@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib
In directory dev.open-bio.org:/tmp/cvs-serv16153

Modified Files:
      Tag: BRANCH-biohackathon2008
	bio.rb 
Log Message:
Fixed bug in formatting features when exporting to EMBL.


Index: bio.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio.rb,v
retrieving revision 1.89.2.1
retrieving revision 1.89.2.2
diff -C2 -d -r1.89.2.1 -r1.89.2.2
*** bio.rb	20 Feb 2008 09:56:22 -0000	1.89.2.1
--- bio.rb	20 Feb 2008 13:54:19 -0000	1.89.2.2
***************
*** 280,284 ****
  class String
    def fold(width = 80)
!     self.gsub(Regexp.new("(.{1,#{width}})"), "\\1\n")
    end
    
--- 280,284 ----
  class String
    def fold(width = 80)
!     self.gsub(Regexp.new("(.{1,#{width}})"), "\\1\n").sub(/\n$/, '')
    end
    
***************
*** 308,310 ****
      return result_string
    end
! end
\ No newline at end of file
--- 308,310 ----
      return result_string
    end
! end



From aerts at dev.open-bio.org  Wed Feb 20 13:54:21 2008
From: aerts at dev.open-bio.org (Jan Aerts)
Date: Wed, 20 Feb 2008 13:54:21 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/sequence format.rb,1.4.2.4,1.4.2.5
Message-ID: <200802201354.m1KDsLWx016180@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/sequence
In directory dev.open-bio.org:/tmp/cvs-serv16153/bio/sequence

Modified Files:
      Tag: BRANCH-biohackathon2008
	format.rb 
Log Message:
Fixed bug in formatting features when exporting to EMBL.


Index: format.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence/format.rb,v
retrieving revision 1.4.2.4
retrieving revision 1.4.2.5
diff -C2 -d -r1.4.2.4 -r1.4.2.5
*** format.rb	20 Feb 2008 09:56:22 -0000	1.4.2.4
--- format.rb	20 Feb 2008 13:54:19 -0000	1.4.2.5
***************
*** 47,51 ****
--- 47,53 ----
        end
  
+       result << "\n"
        result << format_qualifiers(feature.qualifiers, indent, width)
+       result << "\n"
      end
      return result
***************
*** 62,66 ****
          lines = ('/' + q + '="' + v + '"').fold(width)
        else
!         if v[/\D/]
            #v.delete!("\x00-\x1f\x7f-\xff")
            v.gsub!(/"/, '""')
--- 64,68 ----
          lines = ('/' + q + '="' + v + '"').fold(width)
        else
!         if ( v[/\D/] or q == 'chromosome' )
            #v.delete!("\x00-\x1f\x7f-\xff")
            v.gsub!(/"/, '""')
***************
*** 72,76 ****
        lines.gsub!(/^/, indent)
        lines
!     end.join
    end
  
--- 74,78 ----
        lines.gsub!(/^/, indent)
        lines
!     end.join("\n")
    end
  



From ngoto at dev.open-bio.org  Wed Feb 20 17:04:49 2008
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Wed, 20 Feb 2008 17:04:49 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio reference.rb,1.24.2.1,1.24.2.2
Message-ID: <200802201704.m1KH4nCF017912@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv17810/lib/bio

Modified Files:
      Tag: BRANCH-biohackathon2008
	reference.rb 
Log Message:
Bio::References#new is added not to create Bio::References instances anymore.
New transitional module Bio::References::BackwardCompatibilityForBioReferences 
is added to help keeping backward compatibility.
(The only reason why not to erase Bio::References class is to load
Marshal.dump data.)


Index: reference.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/reference.rb,v
retrieving revision 1.24.2.1
retrieving revision 1.24.2.2
diff -C2 -d -r1.24.2.1 -r1.24.2.2
*** reference.rb	18 Feb 2008 15:44:39 -0000	1.24.2.1
--- reference.rb	20 Feb 2008 17:04:47 -0000	1.24.2.2
***************
*** 580,587 ****
--- 580,593 ----
    # = DESCRIPTION
    #
+   # This class is OBSOLETED, and will soon be removed.
+   # Instead of this class, an array is to be used.
+   #
+   # 
    # A container class for Bio::Reference objects.
    #
    # = USAGE
    #
+   # This class should NOT be used.
+   #
    #   refs = Bio::References.new
    #   refs.append(Bio::Reference.new(hash))
***************
*** 591,596 ****
    #
    class References
!     include Enumerable
!     
      # Array of Bio::Reference objects
      attr_accessor :references
--- 597,638 ----
    #
    class References
! 
!     # module to keep backward compatibility with obsoleted Bio::References
!     module BackwardCompatibilityForBioReferences #:nodoc:
! 
!       # Backward compatibility with Bio::References#references.
!       # Now, references are stored in an array, and
!       # you should change your code not to use this method.
!       def references
!         warn 'Bio::References is obsoleted. Now, references are stored in an array.'
!         self
!       end
! 
!       # Backward compatibility with Bio::References#append.
!       # Now, references are stored in an array, and
!       # you should change your code not to use this method.
!       def append(reference)
!         warn 'Bio::References is obsoleted. Now, references are stored in an array.'
!         self.push(reference) if reference.is_a? Reference
!         self
!       end
!     end #module BackwardCompatibilityForBioReferences
! 
!     # This method should not be used.
!     # Only for backward compatibility of existing code.
!     #
!     # Since Bio::References is obsoleted,
!     # Bio::References.new not returns Bio::References object,
!     # but modifies given _ary_ and returns the _ary_.
!     #
!     # *Arguments*:
!     # * (optional) __: Array of Bio::Reference objects
!     # *Returns*:: the given array
!     def self.new(ary = [])
!       warn 'Bio::References is obsoleted. Some methods are added to given array to keep backward compatibility.'
!       ary.extend(BackwardCompatibilityForBioReferences)
!       ary
!     end
! 
      # Array of Bio::Reference objects
      attr_accessor :references



From ngoto at dev.open-bio.org  Fri Feb 22 14:26:18 2008
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Fri, 22 Feb 2008 14:26:18 +0000
Subject: [BioRuby-cvs] bioruby/lib bio.rb,1.89.2.2,1.89.2.3
Message-ID: <200802221426.m1MEQI5W030582@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib
In directory dev.open-bio.org:/tmp/cvs-serv30562

Modified Files:
      Tag: BRANCH-biohackathon2008
	bio.rb 
Log Message:
reverted to 1.89


Index: bio.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio.rb,v
retrieving revision 1.89.2.2
retrieving revision 1.89.2.3
diff -C2 -d -r1.89.2.2 -r1.89.2.3
*** bio.rb	20 Feb 2008 13:54:19 -0000	1.89.2.2
--- bio.rb	22 Feb 2008 14:26:16 -0000	1.89.2.3
***************
*** 278,310 ****
  end
  
- class String
-   def fold(width = 80)
-     self.gsub(Regexp.new("(.{1,#{width}})"), "\\1\n").sub(/\n$/, '')
-   end
-   
-   def wrap(width = 80, prefix = '')
-     actual_width = width - prefix.length
-     result = []
-     left = self.dup
-     while left and left.length > actual_width
-       line = nil
-       actual_width.downto(1) do |i|
-         if left[i..i] == ' ' or /[,;]/ =~ left[(i-1)..(i-1)]  then
-           line = left[0..(i-1)].sub(/ +\z/, '')
-           left = left[i..-1].sub(/\A +/, '')
-           break
-         end
-       end
-       if line.nil? then
-         line = left[0..(actual_width-1)]
-         left = left[actual_width..-1]
-       end
-       result << line
-     end
-     result << left if left
-     result_string = result.join("\n#{prefix}")
-     result_string = prefix + result_string unless result_string.empty?
- #    result_string << "\n" unless result_string.empty?
-     return result_string
-   end
- end
--- 278,279 ----



From ngoto at dev.open-bio.org  Fri Feb 22 14:30:46 2008
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Fri, 22 Feb 2008 14:30:46 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/sequence format.rb,1.4.2.5,1.4.2.6
Message-ID: <200802221430.m1MEUknT030652@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/sequence
In directory dev.open-bio.org:/tmp/cvs-serv30611

Modified Files:
      Tag: BRANCH-biohackathon2008
	format.rb 
Log Message:
 * fold() and wrap() are reverted
 * Bug fix in format_features() and format_qualifiers()
 * The content of 'translate' qualifier is now wrapped by double quote


Index: format.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence/format.rb,v
retrieving revision 1.4.2.5
retrieving revision 1.4.2.6
diff -C2 -d -r1.4.2.5 -r1.4.2.6
*** format.rb	20 Feb 2008 13:54:19 -0000	1.4.2.5
--- format.rb	22 Feb 2008 14:30:44 -0000	1.4.2.6
***************
*** 31,34 ****
--- 31,109 ----
  #   puts s.output(:embl)
  module Format
+ 
+   # INTERNAL USE ONLY, YOU SHOULD NOT CALL THIS METHOD. (And in any
+   # case, it would be difficult to successfully call this method outside
+   # its expected context).
+   #
+   # Output the FASTA format string of the sequence.  
+   #
+   # UNFORTUNATLY, the current implementation of Bio::Sequence is incapable of 
+   # using either the header or width arguments.  So something needs to be
+   # changed...
+   #
+   # Currently, this method is used in Bio::Sequence#output like so,
+   #
+   #   s = Bio::Sequence.new('atgc')
+   #   puts s.output(:fasta)                   #=> "> \natgc\n"
+   # ---
+   # *Arguments*:
+   # * (optional) _header_: String (default nil)
+   # * (optional) _width_: Fixnum (default nil)
+   # *Returns*:: String object
+   def format_fasta(header = nil, width = nil)
+     header ||= "#{@entry_id} #{@definition}"
+ 
+     ">#{header}\n" +
+     if width
+       @seq.to_s.gsub(Regexp.new(".{1,#{width}}"), "\\0\n")
+     else
+       @seq.to_s + "\n"
+     end
+   end
+ 
+   #---
+ 
+   # Not yet implemented :)
+   # Remove the nodoc command after implementation!
+   # ---
+   # *Returns*:: String object
+   #def format_gff #:nodoc:
+   #  raise NotImplementedError
+   #end
+ 
+   # INTERNAL USE ONLY, YOU SHOULD NOT CALL THIS METHOD. (And in any
+   # case, it would be difficult to successfully call this method outside
+   # its expected context).
+   #
+   # Output the Genbank format string of the sequence.  
+   # Used in Bio::Sequence#output.
+   # ---
+   # *Returns*:: String object
+   #def format_genbank
+   #  prefix = ' ' * 5
+   #  indent = prefix + ' ' * 16
+   #  fwidth = 79 - indent.length
+   #
+   #  format_features(prefix, indent, fwidth)
+   #end
+ 
+   # INTERNAL USE ONLY, YOU SHOULD NOT CALL THIS METHOD. (And in any
+   # case, it would be difficult to successfully call this method outside
+   # its expected context).
+   #
+   # Output the EMBL format string of the sequence.  
+   # Used in Bio::Sequence#output.
+   # ---
+   # *Returns*:: String object
+   #def format_embl
+   #  prefix = 'FT   '
+   #  indent = prefix + ' ' * 16
+   #  fwidth = 80 - indent.length
+   #
+   #  format_features(prefix, indent, fwidth)
+   #end
+ 
+   #+++
+ 
    private
  
***************
*** 42,53 ****
  
        head = ''
!       (position).wrap(width).each_line do |line|
          result << head << line
          head = indent
        end
  
-       result << "\n"
        result << format_qualifiers(feature.qualifiers, indent, width)
-       result << "\n"
      end
      return result
--- 117,126 ----
  
        head = ''
!       wrap(position, width).each_line do |line|
          result << head << line
          head = indent
        end
  
        result << format_qualifiers(feature.qualifiers, indent, width)
      end
      return result
***************
*** 60,80 ****
  
        if v == true
!         lines =('/' + q).wrap(width)
        elsif q == 'translation'
!         lines = ('/' + q + '="' + v + '"').fold(width)
        else
!         if ( v[/\D/] or q == 'chromosome' )
            #v.delete!("\x00-\x1f\x7f-\xff")
            v.gsub!(/"/, '""')
            v = '"' + v + '"'
          end
!         lines = ('/' + q + '=' + v).wrap(width)
        end
  
        lines.gsub!(/^/, indent)
        lines
!     end.join("\n")
    end
  
  
  end # Format
--- 133,180 ----
  
        if v == true
!         lines = wrap('/' + q, width)
        elsif q == 'translation'
!         lines = fold("/#{q}=\"#{v}\"", width)
        else
!         if v[/\D/] or q == 'chromosome'
            #v.delete!("\x00-\x1f\x7f-\xff")
            v.gsub!(/"/, '""')
            v = '"' + v + '"'
          end
!         lines = wrap('/' + q + '=' + v, width)
        end
  
        lines.gsub!(/^/, indent)
        lines
!     end.join
!   end
! 
!   def fold(str, width)
!     str.gsub(Regexp.new("(.{1,#{width}})"), "\\1\n")
    end
  
+   def wrap(str, width)
+     result = []
+     left = str.dup
+     while left and left.length > width
+       line = nil
+       width.downto(1) do |i|
+         if left[i..i] == ' ' or /[\,\;]/ =~ left[(i-1)..(i-1)]  then
+           line = left[0..(i-1)].sub(/ +\z/, '')
+           left = left[i..-1].sub(/\A +/, '')
+           break
+         end
+       end
+       if line.nil? then
+         line = left[0..(width-1)]
+         left = left[width..-1]
+       end
+       result << line
+     end
+     result << left if left
+     result_string = result.join("\n")
+     result_string << "\n" unless result_string.empty?
+     return result_string
+   end
  
  end # Format



From ngoto at dev.open-bio.org  Thu Feb 28 05:51:05 2008
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Thu, 28 Feb 2008 05:51:05 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio reference.rb,1.24.2.2,1.24.2.3
Message-ID: <200802280551.m1S5p5eX020471@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv20451

Modified Files:
      Tag: BRANCH-biohackathon2008
	reference.rb 
Log Message:
@sequence_position should be nil if no information available


Index: reference.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/reference.rb,v
retrieving revision 1.24.2.2
retrieving revision 1.24.2.3
diff -C2 -d -r1.24.2.2 -r1.24.2.3
*** reference.rb	20 Feb 2008 17:04:47 -0000	1.24.2.2
--- reference.rb	28 Feb 2008 05:51:03 -0000	1.24.2.3
***************
*** 138,142 ****
        @mesh     = hash['mesh']
        @embl_gb_record_number = hash['embl_gb_record_number'] || nil
!       @sequence_position = hash['sequence_position'] || []
        @comments = hash['comments'] || []
        @xrefs    = hash['xrefs'] || []
--- 138,142 ----
        @mesh     = hash['mesh']
        @embl_gb_record_number = hash['embl_gb_record_number'] || nil
!       @sequence_position = hash['sequence_position'] || nil
        @comments = hash['comments'] || []
        @xrefs    = hash['xrefs'] || []
***************
*** 280,284 ****
          end
        end
!       if @sequence_position != ''
          lines << "RP   #{@sequence_position}"
        end
--- 280,284 ----
          end
        end
!       if ! @sequence_position.nil?
          lines << "RP   #{@sequence_position}"
        end



From ngoto at dev.open-bio.org  Thu Feb 28 05:54:53 2008
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Thu, 28 Feb 2008 05:54:53 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/db/genbank common.rb,1.11,1.11.2.1
Message-ID: <200802280554.m1S5sr5Z020520@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/db/genbank
In directory dev.open-bio.org:/tmp/cvs-serv20500/db/genbank

Modified Files:
      Tag: BRANCH-biohackathon2008
	common.rb 
Log Message:
changed to parse sequence position and reference number in REFERENCES


Index: common.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/genbank/common.rb,v
retrieving revision 1.11
retrieving revision 1.11.2.1
diff -C2 -d -r1.11 -r1.11.2.1
*** common.rb	5 Apr 2007 23:35:40 -0000	1.11
--- common.rb	28 Feb 2008 05:54:51 -0000	1.11.2.1
***************
*** 141,144 ****
--- 141,149 ----
          subtag2array(ref).each do |field|
            case tag_get(field)
+           when /^\s*REFERENCE\s+(\d+)(\s+\(bases\s+(\d+)\s+to\s+(\d+)\))?/
+             hash['embl_gb_record_number'] = $1.to_i
+             if $2 then
+               hash['sequence_position'] = "#{$3}-#{$4}"
+             end
            when /AUTHORS/
              authors = truncate(tag_cut(field))



From pjotr at dev.open-bio.org  Sat Feb  2 13:03:36 2008
From: pjotr at dev.open-bio.org (Pjotr Prins)
Date: Sat, 02 Feb 2008 13:03:36 -0000
Subject: [BioRuby-cvs] bioruby/doc Tutorial.rd,1.13,1.14
Message-ID: <200802021303.m12D3PNX031194@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/doc
In directory dev.open-bio.org:/tmp/cvs-serv31174

Modified Files:
	Tutorial.rd 
Log Message:
Tabs in the Tutorial broke the rd parser - the Wiki will be fixed now.



Index: Tutorial.rd
===================================================================
RCS file: /home/repository/bioruby/bioruby/doc/Tutorial.rd,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** Tutorial.rd	9 Jul 2007 12:28:07 -0000	1.13
--- Tutorial.rd	2 Feb 2008 13:03:23 -0000	1.14
***************
*** 1,2 ****
--- 1,10 ----
+ # This document is generated with a version of rd2html (part of Hiki)
+ #
+ # A possible test run could be from rdtool:
+ #
+ #   ruby -I lib ./bin/rd2 ~/izip/cvs/opensource/bioruby/doc/Tutorial.rd
+ #
+ # A common problem is tabs in the text file!
+ 
  =begin
  
***************
*** 5,13 ****
    $Id$
  
! Translated into English: Naohisa Goto <ng at bioruby.org>
  
! Editor:                  PjotrPrins <p at bioruby.org>
  
! Copyright (C) 2001-2003 KATAYAMA Toshiaki <k at bioruby.org>, 2005-2007 Pjotr Prins, Naohisa Goto and others
  
  IMPORTANT NOTICE: This page is maintained in the BioRuby CVS
--- 13,21 ----
    $Id$
  
! Translated into English: Naohisa Goto <ng .at. bioruby.org>
  
! Editor:                  PjotrPrins <p .at. bioruby.org>
  
! Copyright (C) 2001-2003 KATAYAMA Toshiaki <k .at. bioruby.org>, 2005-2008 Pjotr Prins, Naohisa Goto and others
  
  IMPORTANT NOTICE: This page is maintained in the BioRuby CVS
***************
*** 32,36 ****
  version it has with the
  
! 	% ruby -v
  
  command. Showing something like:
--- 40,44 ----
  version it has with the
  
!   % ruby -v
  
  command. Showing something like:
***************
*** 55,59 ****
    bioruby> puts seq
    atgcatgcaaaa
!   bioruby> puts seq.complement 
    ttttgcatgcat
  
--- 63,67 ----
    bioruby> puts seq
    atgcatgcaaaa
!   bioruby> puts seq.complement
    ttttgcatgcat
  
***************
*** 94,98 ****
      puts seq.complement.translate       # translation of complemental strand
  
! 		counts = {'a'=>seq.count('a'),'c'=>seq.count('c'),'g'=>seq.count('g'),'t'=>seq.count('t')}
      p randomseq = Bio::Sequence::NA.randomize(counts)  # reshuffle sequence with same freq.
  
--- 102,106 ----
      puts seq.complement.translate       # translation of complemental strand
  
!     counts = {'a'=>seq.count('a'),'c'=>seq.count('c'),'g'=>seq.count('g'),'t'=>seq.count('t')}
      p randomseq = Bio::Sequence::NA.randomize(counts)  # reshuffle sequence with same freq.
  
***************
*** 159,163 ****
  * Divide a genome sequence into sections of 10000bp and
    output FASTA formatted sequences. The 1000bp at the start and end of
! 	each subsequence overlapped. At the 3' end of the sequence the
    leftover subsequence shorter than 10000bp is also added
  
--- 167,171 ----
  * Divide a genome sequence into sections of 10000bp and
    output FASTA formatted sequences. The 1000bp at the start and end of
!   each subsequence overlapped. At the 3' end of the sequence the
    leftover subsequence shorter than 10000bp is also added
  
***************
*** 252,258 ****
  
      #!/usr/bin/env ruby
!   
      require 'bio'
!     
      ff = Bio::FlatFile.new(Bio::GenBank, ARGF)
      ff.each_entry do |gb|
--- 260,266 ----
  
      #!/usr/bin/env ruby
! 
      require 'bio'
! 
      ff = Bio::FlatFile.new(Bio::GenBank, ARGF)
      ff.each_entry do |gb|
***************
*** 470,475 ****
  
    rebase = Bio::RestrictionEnzyme.rebase
! 	rebase.each do |enzyme_name, info|
! 		p enzyme_name
    end
  
--- 478,483 ----
  
    rebase = Bio::RestrictionEnzyme.rebase
!   rebase.each do |enzyme_name, info|
!     p enzyme_name
    end
  
***************
*** 483,488 ****
        end
     end
! 	 res.each do |frag|
! 	    em = EnzymeMatch.new
  
        em.p_left = frag.p_left
--- 491,496 ----
        end
     end
!    res.each do |frag|
!       em = EnzymeMatch.new
  
        em.p_left = frag.p_left
***************
*** 494,498 ****
        em.enzyme = ar_enz
        em.sequence = ar_seq
! 			p em
      end
  
--- 502,506 ----
        em.enzyme = ar_enz
        em.sequence = ar_seq
!       p em
      end
  
***************
*** 1160,1168 ****
  == Comparing BioProjects
  
! For a quick functional comparison of BioRuby, BioPerl, BioPython and Bioconductor (R) see ((<http://sciruby.codeforpeople.com/sr.cgi/BioProjects>))
  
  == Using BioRuby with R
  
! Using Ruby with R Pjotr wrote a section on SciRuby. See ((<ULR:http://sciruby.codeforpeople.com/sr.cgi/RubyWithRlang>))
  
  == Using BioPerl or BioPython from Ruby
--- 1168,1176 ----
  == Comparing BioProjects
  
! For a quick functional comparison of BioRuby, BioPerl, BioPython and Bioconductor (R) see ((<URL:http://sciruby.codeforpeople.com/sr.cgi/BioProjects>))
  
  == Using BioRuby with R
  
! Using Ruby with R Pjotr wrote a section on SciRuby. See ((<URL:http://sciruby.codeforpeople.com/sr.cgi/RubyWithRlang>))
  
  == Using BioPerl or BioPython from Ruby
***************
*** 1182,1184 ****
  
  =end
- 
--- 1190,1191 ----



From pjotr at dev.open-bio.org  Sat Feb  2 14:02:03 2008
From: pjotr at dev.open-bio.org (Pjotr Prins)
Date: Sat, 02 Feb 2008 14:02:03 -0000
Subject: [BioRuby-cvs] bioruby/doc Tutorial.rd,1.14,1.15
Message-ID: <200802021401.m12E1uuN031293@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/doc
In directory dev.open-bio.org:/tmp/cvs-serv31273

Modified Files:
	Tutorial.rd 
Log Message:
Updating tutorial

Index: Tutorial.rd
===================================================================
RCS file: /home/repository/bioruby/bioruby/doc/Tutorial.rd,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** Tutorial.rd	2 Feb 2008 13:03:23 -0000	1.14
--- Tutorial.rd	2 Feb 2008 14:01:54 -0000	1.15
***************
*** 3,7 ****
  # A possible test run could be from rdtool:
  #
! #   ruby -I lib ./bin/rd2 ~/izip/cvs/opensource/bioruby/doc/Tutorial.rd
  #
  # A common problem is tabs in the text file!
--- 3,12 ----
  # A possible test run could be from rdtool:
  #
! #   ruby -I lib ./bin/rd2 ~/cvs/opensource/bioruby/doc/Tutorial.rd
! #
! # or with style sheet:
! #
! #   ruby -I lib ./bin/rd2 -r rd/rd2html-lib.rb --with-c
! ss=bioruby.css ~/cvs/opensource/bioruby/doc/Tutorial.rd > ~/bioruby.html
  #
  # A common problem is tabs in the text file!
***************
*** 9,39 ****
  =begin
  
! See the document in the CVS repository ./doc/((<Tutorial.rd|URL:http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/*checkout*/bioruby/doc/Tutorial.rd?rev=HEAD&cvsroot=bioruby&content-type=text/plain>)) - for a potentially more up-to-date edition. This one was updated:
! 
!   $Id$
  
! Translated into English: Naohisa Goto <ng .at. bioruby.org>
  
! Editor:                  PjotrPrins <p .at. bioruby.org>
  
! Copyright (C) 2001-2003 KATAYAMA Toshiaki <k .at. bioruby.org>, 2005-2008 Pjotr Prins, Naohisa Goto and others
  
! IMPORTANT NOTICE: This page is maintained in the BioRuby CVS
! repository. Please edit the file there otherwise changes may get
! lost. See ((<BioRuby Developer Information>)) for CVS and mailing list
! access.
  
! = BioRuby Tutorial
  
  == Introduction
  
! This is a tutorial for using Bioruby. For BioRuby you need to install
! Ruby and the BioRuby package on your computer. For each following the
! instruction on the respective websites. (EDITOR's NOTE: include URL's)
! 
! (EDITOR's NOTE: describe rdoc use for individual classes)
  
! For further information on the Ruby language see the section 'Further
! reading' at the end.
  
  You can check whether Ruby is installed on your computer and what
--- 14,40 ----
  =begin
  
! = BioRuby Tutorial
  
! Editor: PjotrPrins <p .at. bioruby.org>
  
! * Copyright (C) 2001-2003 KATAYAMA Toshiaki <k .at. bioruby.org>
! * Copyright (C) 2005-2008 Pjotr Prins, Naohisa Goto and others
  
! The latest version resides in the CVS repository ./doc/((<Tutorial.rd|URL:http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/*checkout*/bioruby/doc/Tutorial.rd?rev=HEAD&cvsroot=bioruby&content-type=text/plain>)). This one was updated:
  
!   $Id$ 
  
! in preparation for the ((<BioHackathlon 2008|URL:http://hackathon.dbcls.jp/>))
  
  == Introduction
  
! This is a tutorial for using Bioruby. A basic knowledge of Ruby is required.
! If you want to know more about the programming langauge Ruby we recommend the
! excellent book ((<Programming Ruby|URL:http://www.pragprog.com/titles/ruby>))
! by Dave Thomas and Andy Hunt - some of it is online
! ((<here|URL:http://www.rubycentral.com/pickaxe/>)).
  
! For BioRuby you need to install
! Ruby and the BioRuby package on your computer.
  
  You can check whether Ruby is installed on your computer and what
***************
*** 46,49 ****
--- 47,61 ----
    ruby 1.8.5 (2006-08-25) [powerpc-linux]
  
+ If you see no such thing you'll have to install Ruby using your installation
+ manager. For more information see the
+ ((<Ruby|URL:http://www.ruby-lang.org/en/>)) website.
+ 
+ Once Ruby is works download and install Bioruby using the links on the
+ ((<Bioruby|URL:http://bioruby.org/>)) website.
+ 
+ A lot of BioRuby's documentation exists in the source code and unit tests. To
+ really dive in you will need the latest source code tree. The embedded rdoc
+ documentation can be viewed online at
+ ((<bioruby's rdoc|URL:http://bioruby.org/rdoc/>)). But first lets start!
  
  == Trying Bioruby
***************
*** 52,56 ****
  following command
  
!   $BIORUBY/bin/bioruby
  
  and you should see a prompt
--- 64,68 ----
  following command
  
!   ./bin/bioruby
  
  and you should see a prompt
***************
*** 93,97 ****
      puts seq.translate                  # translation (Bio::Sequence::AA object)
      puts seq.translate(2)               # translation from frame 2 (default is frame 1)
!     puts seq.translate(1,11)            # using codon table No.11 (see http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi)
  
      p seq.translate.codes               # shows three-letter codes (Array)
--- 105,110 ----
      puts seq.translate                  # translation (Bio::Sequence::AA object)
      puts seq.translate(2)               # translation from frame 2 (default is frame 1)
!     puts seq.translate(1,11)            # using codon table No.11 
!                                         # (see http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi)
  
      p seq.translate.codes               # shows three-letter codes (Array)
***************
*** 114,120 ****
    % ri File.open
  
! Nucleic acid sequence is an object of +Bio::Sequence::NA+ class, and
! amino acid sequence is an object of +Bio::Sequence::AA+ class.  Shared
! methods are in the parent +Bio::Sequence+ class.
  
  As Bio::Sequence class inherits Ruby's String class, you can use
--- 127,133 ----
    % ri File.open
  
! Nucleic acid sequence is an object of Bio::Sequence::NA class, and
! amino acid sequence is an object of Bio::Sequence::AA class.  Shared
! methods are in the parent Bio::Sequence class.
  
  As Bio::Sequence class inherits Ruby's String class, you can use
***************
*** 297,303 ****
      end
  
- (TRANSLATOR'S NOTE: Bio::DB.open have not been used so well.)
- (EDITOR's NOTE: Test code)
- 
  Next, we are going to parse the GenBank 'features', which is normally
  very complicated:
--- 310,313 ----
***************
*** 382,387 ****
  
  Databases in BioRuby are essentially accessed like that of GenBank
! with classes like Bio::GenBank, Bio::KEGG::GENES,
! (EDITOR's NOTE: include complete list)
  
  In many cases the Bio::DatabaseClass acts as a factory pattern
--- 392,397 ----
  
  Databases in BioRuby are essentially accessed like that of GenBank
! with classes like Bio::GenBank, Bio::KEGG::GENES. A full list can be found in 
! the ./lib/bio/db directory of the BioRuby source tree.
  
  In many cases the Bio::DatabaseClass acts as a factory pattern
***************
*** 1151,1160 ****
  == Further reading
  
! See the BioRuby in anger Wiki and the class documentation for more
! information on BioRuby.
  
- The best book to get for understanding and getting productive with the
- Ruby language is 'Programming Ruby' by Dave Thomas and Andy
- Hunt. Strongly recommended!
  
  = APPENDIX
--- 1161,1169 ----
  == Further reading
  
! See the BioRuby in anger Wiki.  A lot of BioRuby's documentation exists in the
! source code and unit tests. To really dive in you will need the latest source
! code tree. The embedded rdoc documentation can be viewed online at
! ((<URL:http://bioruby.org/rdoc/>)).
  
  
  = APPENDIX
***************
*** 1189,1191 ****
--- 1198,1207 ----
  carefully that come with each package.
  
+ == Modifying this page
+ 
+ IMPORTANT NOTICE: This page is maintained in the BioRuby CVS
+ repository. Please edit the file there otherwise changes may get
+ lost. See ((<BioRuby Developer Information>)) for CVS and mailing list
+ access.
+ 
  =end



From pjotr at dev.open-bio.org  Sat Feb  2 14:15:19 2008
From: pjotr at dev.open-bio.org (Pjotr Prins)
Date: Sat, 02 Feb 2008 14:15:19 -0000
Subject: [BioRuby-cvs] bioruby/doc Tutorial.rd,1.15,1.16
Message-ID: <200802021415.m12EFAqB031346@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/doc
In directory dev.open-bio.org:/tmp/cvs-serv31326

Modified Files:
	Tutorial.rd 
Log Message:
Modified tutorial

Index: Tutorial.rd
===================================================================
RCS file: /home/repository/bioruby/bioruby/doc/Tutorial.rd,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** Tutorial.rd	2 Feb 2008 14:01:54 -0000	1.15
--- Tutorial.rd	2 Feb 2008 14:15:08 -0000	1.16
***************
*** 115,120 ****
      puts seq.complement.translate       # translation of complemental strand
  
!     counts = {'a'=>seq.count('a'),'c'=>seq.count('c'),'g'=>seq.count('g'),'t'=>seq.count('t')}
!     p randomseq = Bio::Sequence::NA.randomize(counts)  # reshuffle sequence with same freq.
  
  The p, print and puts methods are standard Ruby ways of outputting to
--- 115,122 ----
      puts seq.complement.translate       # translation of complemental strand
  
!     # reshuffle sequence with same frequencies:
!     counts = {'a'=>seq.count('a'),'c'=>seq.count('c'),
!               'g'=>seq.count('g'),'t'=>seq.count('t')}
!     p randomseq = Bio::Sequence::NA.randomize(counts)  
  
  The p, print and puts methods are standard Ruby ways of outputting to
***************
*** 265,269 ****
        print ">#{gb.accession} "         # Accession
        puts gb.definition                # Definition
!       puts gb.naseq                     # Nucleic acid sequence (Bio::Sequence::NA object)
      end
  
--- 267,272 ----
        print ">#{gb.accession} "         # Accession
        puts gb.definition                # Definition
!       puts gb.naseq                     # Nucleic acid sequence 
!                                         # (Bio::Sequence::NA object)
      end
  
***************
*** 387,391 ****
      aaseq.splicing('21..119')
  
- (EDITOR's NOTE: why use STRINGs here?)
  
  === More databases
--- 390,393 ----
***************
*** 494,498 ****
  and cut a sequence with an enzyme follow up with:
  
!    res = seq.cut_with_enzyme('EcoRII', {:max_permutations => 0}, {:view_ranges => true})
     if res.kind_of? Symbol #error
        err = Err.find_by_code(res.to_s)
--- 496,501 ----
  and cut a sequence with an enzyme follow up with:
  
!    res = seq.cut_with_enzyme('EcoRII', {:max_permutations => 0}, 
!      {:view_ranges => true})
     if res.kind_of? Symbol #error
        err = Err.find_by_code(res.to_s)
***************
*** 529,534 ****
  fasta34. FASTA can be downloaded from ftp://ftp.virginia.edu/pub/fasta/).
  First, you must prepare your FASTA-formatted database sequence file
! target.pep and FASTA-formatted query.pep.  (TRANSLATOR'S NOTE: I think
! we should provide sample data to readers.)
  
      #!/usr/bin/env ruby
--- 532,536 ----
  fasta34. FASTA can be downloaded from ftp://ftp.virginia.edu/pub/fasta/).
  First, you must prepare your FASTA-formatted database sequence file
! target.pep and FASTA-formatted query.pep. 
  
      #!/usr/bin/env ruby
***************
*** 536,547 ****
      require 'bio'
  
!     # Creates FASTA factory object ("ssearch" instead of "fasta34" can also work)
      factory = Bio::Fasta.local('fasta34', ARGV.pop)
      (EDITOR's NOTE: not consistent pop command)
  
-     # Reads FASTA-formatted files (TRANSLATOR'S NOTE: something wrong in Japanese text)
      ff = Bio::FlatFile.new(Bio::FastaFormat, ARGF)
  
!     # Iterates over each entry. the variable "entry" is a Bio::FastaFormat object.
      ff.each do |entry|
        # shows definition line (begins with '>') to the standard error output
--- 538,550 ----
      require 'bio'
  
!     # Creates FASTA factory object ("ssearch" instead of 
!     # "fasta34" can also work)
      factory = Bio::Fasta.local('fasta34', ARGV.pop)
      (EDITOR's NOTE: not consistent pop command)
  
      ff = Bio::FlatFile.new(Bio::FastaFormat, ARGF)
  
!     # Iterates over each entry. the variable "entry" is a 
!     # Bio::FastaFormat object:
      ff.each do |entry|
        # shows definition line (begins with '>') to the standard error output
***************
*** 555,559 ****
          # If E-value is smaller than 0.0001
          if hit.evalue < 0.0001
!           # shows identifier of query and hit, E-value, start and end positions of homologous region (TRANSLATOR'S NOTE: should I change Japanese document?)
            print "#{hit.query_id} : evalue #{hit.evalue}\t#{hit.target_id} at "
            p hit.lap_at
--- 558,563 ----
          # If E-value is smaller than 0.0001
          if hit.evalue < 0.0001
!           # shows identifier of query and hit, E-value, start and 
!           # end positions of homologous region 
            print "#{hit.query_id} : evalue #{hit.evalue}\t#{hit.target_id} at "
            p hit.lap_at
***************
*** 569,573 ****
  FASTA many times easily. Instead of using Fasta#query method,
  Bio::Sequence#fasta method can be used.
- (TRANSLATOR'S NOTE: Bio::Sequence#fasta are not so frequently used.)
  
      seq = ">test seq\nYQVLEEIGRGSFGSVRKVIHIPTKKLLVRKDIKYGHMNSKE"
--- 573,576 ----
***************
*** 585,589 ****
  with the Report object. For example, getting information for hits:
  
- 
      report.each do |hit|
        puts hit.evalue           # E-value
--- 588,591 ----
***************
*** 594,606 ****
        puts hit.query_def        # definition(comment line) of query sequence
        puts hit.query_len        # length of query sequence
!       puts hit.query_seq        # query sequence (TRANSLATOR'S NOTE: sequence of homologous region of query sequence)
        puts hit.target_id        # identifier of hit sequence
        puts hit.target_def       # definition(comment line) of hit sequence
        puts hit.target_len       # length of hit sequence
!       puts hit.target_seq       # hit sequence (TRANSLATOR'S NOTE: sequence of homologous region of hit sequence)
!       puts hit.query_start      # start position of homologous region in query sequence
!       puts hit.query_end        # end position of homologous region in query sequence
!       puts hit.target_start     # start posiotion of homologous region in hit(target) sequence
!       puts hit.target_end       # end position of homologous region in hit(target) sequence
        puts hit.lap_at           # array of above four numbers
      end
--- 596,612 ----
        puts hit.query_def        # definition(comment line) of query sequence
        puts hit.query_len        # length of query sequence
!       puts hit.query_seq        # sequence of homologous region
        puts hit.target_id        # identifier of hit sequence
        puts hit.target_def       # definition(comment line) of hit sequence
        puts hit.target_len       # length of hit sequence
!       puts hit.target_seq       # hit of homologous region of hit sequence
!       puts hit.query_start      # start position of homologous 
!                                 # region in query sequence
!       puts hit.query_end        # end position of homologous region 
!                                 # in query sequence
!       puts hit.target_start     # start posiotion of homologous region 
!                                 # in hit(target) sequence
!       puts hit.target_end       # end position of homologous region 
!                                 # in hit(target) sequence
        puts hit.lap_at           # array of above four numbers
      end
***************
*** 695,717 ****
  
      report.each do |hit|
!       puts hit.bit_score        # bit score (*)
!       puts hit.query_seq        # query sequence (TRANSLATOR'S NOTE: sequence of homologous region of query sequence)
!       puts hit.midline          # middle line string of alignment of homologous region (*)
!       puts hit.target_seq       # hit sequence (TRANSLATOR'S NOTE: sequence of homologous region of query sequence)
  
!       puts hit.evalue           # E-value
!       puts hit.identity         # % identity
!       puts hit.overlap          # length of overlapping region
!       puts hit.query_id         # identifier of query sequence
!       puts hit.query_def        # definition(comment line) of query sequence
!       puts hit.query_len        # length of query sequence
!       puts hit.target_id        # identifier of hit sequence
!       puts hit.target_def       # definition(comment line) of hit sequence
!       puts hit.target_len       # length of hit sequence
!       puts hit.query_start      # start position of homologous region in query sequence
!       puts hit.query_end        # end position of homologous region in query sequence
!       puts hit.target_start     # start position of homologous region in hit(target) sequence
!       puts hit.target_end       # end position of homologous region in hit(target) sequence
!       puts hit.lap_at           # array of above four numbers
      end
  
--- 701,723 ----
  
      report.each do |hit|
!       puts hit.bit_score       
!       puts hit.query_seq       
!       puts hit.midline         
!       puts hit.target_seq      
  
!       puts hit.evalue          
!       puts hit.identity        
!       puts hit.overlap         
!       puts hit.query_id        
!       puts hit.query_def       
!       puts hit.query_len       
!       puts hit.target_id       
!       puts hit.target_def      
!       puts hit.target_len      
!       puts hit.query_start     
!       puts hit.query_end       
!       puts hit.target_start    
!       puts hit.target_end      
!       puts hit.lap_at          
      end
  
***************
*** 1171,1175 ****
  == KEGG API
  
! Please refer to KEGG_API.rd.ja (TRANSLATOR'S NOTE: English version: ((<URL:http://www.genome.jp/kegg/soap/doc/keggapi_manual.html>)) ) and
  
    * ((<URL:http://www.genome.jp/kegg/soap/>))
--- 1177,1181 ----
  == KEGG API
  
! Please refer to KEGG_API.rd.ja (English version: ((<URL:http://www.genome.jp/kegg/soap/doc/keggapi_manual.html>)) ) and
  
    * ((<URL:http://www.genome.jp/kegg/soap/>))



From pjotr at dev.open-bio.org  Sun Feb  3 17:17:59 2008
From: pjotr at dev.open-bio.org (Pjotr Prins)
Date: Sun, 03 Feb 2008 17:17:59 -0000
Subject: [BioRuby-cvs] bioruby/doc Tutorial.rd,1.16,1.17
Message-ID: <200802031717.m13HHoa6015904@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/doc
In directory dev.open-bio.org:/tmp/cvs-serv15881/doc

Modified Files:
	Tutorial.rd 
Log Message:
More doctests in Tutorial.rd

Index: Tutorial.rd
===================================================================
RCS file: /home/repository/bioruby/bioruby/doc/Tutorial.rd,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** Tutorial.rd	2 Feb 2008 14:15:08 -0000	1.16
--- Tutorial.rd	3 Feb 2008 17:17:48 -0000	1.17
***************
*** 13,16 ****
--- 13,17 ----
  
  =begin
+ #doctest Testing bioruby
  
  = BioRuby Tutorial
***************
*** 64,68 ****
  following command
  
!   ./bin/bioruby
  
  and you should see a prompt
--- 65,70 ----
  following command
  
!   ./bin/bioruby  or
!   ruby -I lib bin/bioruby
  
  and you should see a prompt
***************
*** 73,80 ****
  
    bioruby> seq = Bio::Sequence::NA.new("atgcatgcaaaa")
!   bioruby> puts seq
!   atgcatgcaaaa
!   bioruby> puts seq.complement
!   ttttgcatgcat
  
  == Working with nucleic / amino acid sequences (Bio::Sequence class)
--- 75,82 ----
  
    bioruby> seq = Bio::Sequence::NA.new("atgcatgcaaaa")
!   ==> "atgcatgcaaaa"
! 
!   bioruby> seq.complement
!   ==> "ttttgcatgcat"
  
  == Working with nucleic / amino acid sequences (Bio::Sequence class)
***************
*** 89,122 ****
  defined in codontable.rb).
  
  
!     #!/usr/bin/env ruby
! 
!     require 'bio'
! 
!     seq = Bio::Sequence::NA.new("atgcatgcaaaa")
! 
!     puts seq                            # original sequence
!     puts seq.complement                 # complemental sequence (Bio::Sequence::NA object)
!     puts seq.subseq(3,8)                # gets subsequence of positions 3 to 8
  
!     p seq.gc_percent                    # GC percent (BioRuby 0.6.X: Float, BioRuby 0.7 or later: Integer)
!     p seq.composition                   # nucleic acid compositions (Hash)
  
!     puts seq.translate                  # translation (Bio::Sequence::AA object)
!     puts seq.translate(2)               # translation from frame 2 (default is frame 1)
!     puts seq.translate(1,11)            # using codon table No.11 
!                                         # (see http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi)
  
!     p seq.translate.codes               # shows three-letter codes (Array)
!     p seq.translate.names               # shows amino acid names (Array)
!     p seq.translate.composition         # amino acid compositions (Hash)
!     p seq.translate.molecular_weight    # calculating molecular weight (Float)
  
!     puts seq.complement.translate       # translation of complemental strand
  
-     # reshuffle sequence with same frequencies:
-     counts = {'a'=>seq.count('a'),'c'=>seq.count('c'),
-               'g'=>seq.count('g'),'t'=>seq.count('t')}
-     p randomseq = Bio::Sequence::NA.randomize(counts)  
  
  The p, print and puts methods are standard Ruby ways of outputting to
--- 91,136 ----
  defined in codontable.rb).
  
+   bioruby> seq = Bio::Sequence::NA.new("atgcatgcaaaa")
+   ==> "atgcatgcaaaa"
  
!   # complemental sequence (Bio::Sequence::NA object)
!   bioruby> seq.complement
!   ==> "ttttgcatgcat"
  
!   bioruby> seq.subseq(3,8) # gets subsequence of positions 3 to 8
!   ==> "gcatgc"
!   bioruby> seq.gc_percent 
!   ==> 33
!   bioruby> seq.composition 
!   ==> {"a"=>6, "c"=>2, "g"=>2, "t"=>2}
!   bioruby> seq.translate 
!   ==> "MHAK"
!   bioruby> seq.translate(2)        # translate from frame 2
!   ==> "CMQ"
!   bioruby> seq.translate(1,11)     # codon table 11
!   ==> "MHAK"
!   bioruby> seq.translate.codes
!   ==> ["Met", "His", "Ala", "Lys"]
!   bioruby> seq.translate.names
!   ==> ["methionine", "histidine", "alanine", "lysine"]
!   bioruby>  seq.translate.composition
!   ==> {"K"=>1, "A"=>1, "M"=>1, "H"=>1}
!   bioruby> seq.translate.molecular_weight
!   ==> 485.605
!   bioruby> seq.complement.translate
!   ==> "FCMH"
  
! get a random sequence with the same NA count:
  
!   bioruby> counts = {'a'=>seq.count('a'),'c'=>seq.count('c'),'g'=>seq.count('g'),'t'=>seq.count('t')}
!   ==> {"a"=>6, "c"=>2, "g"=>2, "t"=>2}
!   bioruby!> randomseq = Bio::Sequence::NA.randomize(counts) 
!   ==!> "aaacatgaagtc"
  
!   bioruby!> print counts
! a6c2g2t2  
!   bioruby!> p counts
! {"a"=>6, "c"=>2, "g"=>2, "t"=>2}
  
  
  The p, print and puts methods are standard Ruby ways of outputting to
***************
*** 140,152 ****
  has index 0, for example:
  
!   s = 'abc'
!   puts s[0].chr
! 
!   >a
! 
!   puts s[0..1]
! 
!   >ab
! 
  
  So when using String methods, you should subtract 1 from positions
--- 154,163 ----
  has index 0, for example:
  
!   bioruby> s = 'abc'
!   ==> "abc"
!   bioruby> s[0].chr
!   ==> "a"
!   bioruby> s[0..1]
!   ==> "ab"
  
  So when using String methods, you should subtract 1 from positions
***************
*** 160,169 ****
  through a variable named +s+.
  
! * Shows average percentage of GC content for 100 bases (stepping
! the default one base at a time)
  
!     seq.window_search(100) do |s|
!       puts s.gc_percent
!     end
  
  Since the class of each subsequence is the same as original sequence
--- 171,182 ----
  through a variable named +s+.
  
! * Shows average percentage of GC content for 20 bases (stepping the default one base at a time)
  
! bioruby> seq = Bio::Sequence::NA.new("atgcatgcaattaagctaatcccaattagatcatcccgatcatcaaaaaaaaaa")
!   ==> "atgcatgcaattaagctaatcccaattagatcatcccgatcatcaaaaaaaaaa"
! 
!   bioruby>  seq.window_search(20) { |s| print s.gc_percent,',' } 
! 30,35,40,40,35,35,35,30,25,30,30,30,35,35,35,35,35,40,45,45,45,45,40,35,40,40,40,40,40,35,35,35,30,30,30,  ==> ""
!  
  
  Since the class of each subsequence is the same as original sequence
***************
*** 1165,1168 ****
--- 1178,1192 ----
  included - with output)
  
+ == Unit testing and doctests
+ 
+ BioRuby comes with an extensive testing framework with over 1300 tests and 2700
+ assertions. To run the unit tests:
+ 
+   cd test
+   ruby runner.rb
+ 
+ We have also started with doctest for Ruby. We are porting the examples
+ in this tutorial to doctest - more info upcoming.
+ 
  == Further reading
  



From pjotr at dev.open-bio.org  Tue Feb  5 12:01:26 2008
From: pjotr at dev.open-bio.org (Pjotr Prins)
Date: Tue, 05 Feb 2008 12:01:26 -0000
Subject: [BioRuby-cvs] bioruby/doc Tutorial.rd,1.17,1.18
Message-ID: <200802051201.m15C1JTf032112@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/doc
In directory dev.open-bio.org:/tmp/cvs-serv32092/doc

Modified Files:
	Tutorial.rd 
Log Message:
Minor tweak to Tutorial.rd

Index: Tutorial.rd
===================================================================
RCS file: /home/repository/bioruby/bioruby/doc/Tutorial.rd,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -d -r1.17 -r1.18
*** Tutorial.rd	3 Feb 2008 17:17:48 -0000	1.17
--- Tutorial.rd	5 Feb 2008 12:01:16 -0000	1.18
***************
*** 129,135 ****
  
    bioruby!> print counts
! a6c2g2t2  
    bioruby!> p counts
! {"a"=>6, "c"=>2, "g"=>2, "t"=>2}
  
  
--- 129,135 ----
  
    bioruby!> print counts
!   a6c2g2t2  
    bioruby!> p counts
!   {"a"=>6, "c"=>2, "g"=>2, "t"=>2}
  
  
***************
*** 173,183 ****
  * Shows average percentage of GC content for 20 bases (stepping the default one base at a time)
  
! bioruby> seq = Bio::Sequence::NA.new("atgcatgcaattaagctaatcccaattagatcatcccgatcatcaaaaaaaaaa")
    ==> "atgcatgcaattaagctaatcccaattagatcatcccgatcatcaaaaaaaaaa"
  
    bioruby>  seq.window_search(20) { |s| print s.gc_percent,',' } 
! 30,35,40,40,35,35,35,30,25,30,30,30,35,35,35,35,35,40,45,45,45,45,40,35,40,40,40,40,40,35,35,35,30,30,30,  ==> ""
   
- 
  Since the class of each subsequence is the same as original sequence
  (Bio::Sequence::NA or Bio::Sequence::AA or Bio::Sequence), you can
--- 173,182 ----
  * Shows average percentage of GC content for 20 bases (stepping the default one base at a time)
  
!   bioruby> seq = Bio::Sequence::NA.new("atgcatgcaattaagctaatcccaattagatcatcccgatcatcaaaaaaaaaa")
    ==> "atgcatgcaattaagctaatcccaattagatcatcccgatcatcaaaaaaaaaa"
  
    bioruby>  seq.window_search(20) { |s| print s.gc_percent,',' } 
!   30,35,40,40,35,35,35,30,25,30,30,30,35,35,35,35,35,40,45,45,45,45,40,35,40,40,40,40,40,35,35,35,30,30,30,  ==> ""
   
  Since the class of each subsequence is the same as original sequence
  (Bio::Sequence::NA or Bio::Sequence::AA or Bio::Sequence), you can



From pjotr at dev.open-bio.org  Tue Feb  5 12:11:20 2008
From: pjotr at dev.open-bio.org (Pjotr Prins)
Date: Tue, 05 Feb 2008 12:11:20 -0000
Subject: [BioRuby-cvs] bioruby/sample gb2fasta.rb,0.5,0.6
Message-ID: <200802051211.m15CBDam032291@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/sample
In directory dev.open-bio.org:/tmp/cvs-serv32271/sample

Modified Files:
	gb2fasta.rb 
Log Message:
Fixed broken require in gb2fasta example

Index: gb2fasta.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/sample/gb2fasta.rb,v
retrieving revision 0.5
retrieving revision 0.6
diff -C2 -d -r0.5 -r0.6
*** gb2fasta.rb	23 Jul 2002 04:51:24 -0000	0.5
--- gb2fasta.rb	5 Feb 2008 12:11:11 -0000	0.6
***************
*** 19,24 ****
  #
  
! require 'bio/io/flatfile'
! require 'bio/db/genbank'
  
  include Bio
--- 19,23 ----
  #
  
! require 'bio'
  
  include Bio



From pjotr at dev.open-bio.org  Wed Feb  6 16:26:05 2008
From: pjotr at dev.open-bio.org (Pjotr Prins)
Date: Wed, 06 Feb 2008 16:26:05 -0000
Subject: [BioRuby-cvs] bioruby/sample na2aa.rb,NONE,1.1
Message-ID: <200802061625.m16GPuIu005441@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/sample
In directory dev.open-bio.org:/tmp/cvs-serv5421

Added Files:
	na2aa.rb 
Log Message:
Simple example to translate any NA to AA fasta

--- NEW FILE: na2aa.rb ---
#!/usr/bin/env ruby
#
# translate.rb - translate any NA input into AA FASTA format
#
#   Copyright (C) 2008 KATAYAMA Toshiaki <k at bioruby.org> & Pjotr Prins
#
#  This program is free software; you can redistribute it and/or modify
#  it under the terms of the GNU General Public License as published by
#  the Free Software Foundation; either version 2 of the License, or
#  (at your option) any later version.
#
#  This program is distributed in the hope that it will be useful,
#  but WITHOUT ANY WARRANTY; without even the implied warranty of
#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#  GNU General Public License for more details.
#
#  $Id: na2aa.rb,v 1.1 2008/02/06 16:25:53 pjotr Exp $
#

require 'bio'
require 'pp'

include Bio

ARGV.each do | fn |
  Bio::FlatFile.auto(fn).each do | item |
    seq = Sequence::NA.new(item.data)
    aa = seq.translate
    aa.gsub!(/X/,'-')
    rec = Bio::FastaFormat.new('> '+item.definition+"\n"+aa)
    print rec
  end
end




From pjotr at dev.open-bio.org  Mon Feb 11 07:08:56 2008
From: pjotr at dev.open-bio.org (Pjotr Prins)
Date: Mon, 11 Feb 2008 07:08:56 -0000
Subject: [BioRuby-cvs] bioruby/doc Tutorial.rd,1.18,1.19
Message-ID: <200802110708.m1B78mwU007283@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/doc
In directory dev.open-bio.org:/tmp/cvs-serv7263/doc

Modified Files:
	Tutorial.rd 
Log Message:
Expanding on the Tutorial

Index: Tutorial.rd
===================================================================
RCS file: /home/repository/bioruby/bioruby/doc/Tutorial.rd,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** Tutorial.rd	5 Feb 2008 12:01:16 -0000	1.18
--- Tutorial.rd	11 Feb 2008 07:08:46 -0000	1.19
***************
*** 1,5 ****
  # This document is generated with a version of rd2html (part of Hiki)
  #
! # A possible test run could be from rdtool:
  #
  #   ruby -I lib ./bin/rd2 ~/cvs/opensource/bioruby/doc/Tutorial.rd
--- 1,5 ----
  # This document is generated with a version of rd2html (part of Hiki)
  #
! # A possible test run could be from rdtool (on Debian package rdtool)
  #
  #   ruby -I lib ./bin/rd2 ~/cvs/opensource/bioruby/doc/Tutorial.rd
***************
*** 10,14 ****
  ss=bioruby.css ~/cvs/opensource/bioruby/doc/Tutorial.rd > ~/bioruby.html
  #
! # A common problem is tabs in the text file!
  
  =begin
--- 10,23 ----
  ss=bioruby.css ~/cvs/opensource/bioruby/doc/Tutorial.rd > ~/bioruby.html
  #
! # in Debian:
! #
! #   rd2 -r rd/rd2html-lib  --with-css="/home/wrk/izip/cvs/opensource/bioruby/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css" Tutorial.rd > index.html
! #
! # A common problem is tabs in the text file! TABs are not allowed.
! #
! # To add tests run Toshiaki's bioruby shell and paste in the query plus
! # results.
! #
! # To run the embedded Ruby doctests you can get the doctest.rb from Pjotr.
  
  =begin
***************
*** 36,41 ****
  ((<here|URL:http://www.rubycentral.com/pickaxe/>)).
  
! For BioRuby you need to install
! Ruby and the BioRuby package on your computer.
  
  You can check whether Ruby is installed on your computer and what
--- 45,49 ----
  ((<here|URL:http://www.rubycentral.com/pickaxe/>)).
  
! For BioRuby you need to install Ruby and the BioRuby package on your computer
  
  You can check whether Ruby is installed on your computer and what
***************
*** 80,83 ****
--- 88,95 ----
    ==> "ttttgcatgcat"
  
+ See the the Bioruby shell section below for more tweaking. If you have trouble running
+ examples also check the section below on trouble shooting. You can also post a 
+ question to the mailing list. BioRuby developers usually try to help.
+ 
  == Working with nucleic / amino acid sequences (Bio::Sequence class)
  
***************
*** 171,181 ****
  through a variable named +s+.
  
! * Shows average percentage of GC content for 20 bases (stepping the default one base at a time)
  
    bioruby> seq = Bio::Sequence::NA.new("atgcatgcaattaagctaatcccaattagatcatcccgatcatcaaaaaaaaaa")
    ==> "atgcatgcaattaagctaatcccaattagatcatcccgatcatcaaaaaaaaaa"
  
!   bioruby>  seq.window_search(20) { |s| print s.gc_percent,',' } 
!   30,35,40,40,35,35,35,30,25,30,30,30,35,35,35,35,35,40,45,45,45,45,40,35,40,40,40,40,40,35,35,35,30,30,30,  ==> ""
   
  Since the class of each subsequence is the same as original sequence
--- 183,195 ----
  through a variable named +s+.
  
! * Show average percentage of GC content for 20 bases (stepping the default one base at a time)
  
    bioruby> seq = Bio::Sequence::NA.new("atgcatgcaattaagctaatcccaattagatcatcccgatcatcaaaaaaaaaa")
    ==> "atgcatgcaattaagctaatcccaattagatcatcccgatcatcaaaaaaaaaa"
  
!   bioruby> a=[]; seq.window_search(20) { |s| a.push s.gc_percent } 
!   bioruby> a
!   ==> [30, 35, 40, 40, 35, 35, 35, 30, 25, 30, 30, 30, 35, 35, 35, 35, 35, 40, 45, 45, 45, 45, 40, 35, 40, 40, 40, 40, 40, 35, 35, 35, 30, 30, 30]
! 
   
  Since the class of each subsequence is the same as original sequence
***************
*** 185,191 ****
  * Shows translation results for 15 bases shifting a codon at a time
  
!     seq.window_search(15, 3) do |s|
!       puts s.translate
!     end
  
  Finally, the window_search method returns the last leftover
--- 199,209 ----
  * Shows translation results for 15 bases shifting a codon at a time
  
!   bioruby> a = []
!   bioruby> seq.window_search(15, 3) do |s|
!   bioruby>   a.push s.translate
!   bioruby> end
!   bioruby> a
!   ==> ["MHAIK", "HAIKL", "AIKLI", "IKLIP", "KLIPI", "LIPIR", "IPIRS", "PIRSS", "IRSSR", "RSSRS", "SSRSS", "SRSSK", "RSSKK", "SSKKK"]
! 
  
  Finally, the window_search method returns the last leftover
***************
*** 193,206 ****
  
  * Divide a genome sequence into sections of 10000bp and
!   output FASTA formatted sequences. The 1000bp at the start and end of
!   each subsequence overlapped. At the 3' end of the sequence the
!   leftover subsequence shorter than 10000bp is also added
  
      i = 1
      remainder = seq.window_search(10000, 9000) do |s|
!       puts s.to_fasta("segment #{i}", 60)
        i += 1
      end
!     puts remainder.to_fasta("segment #{i}", 60)
  
  If you don't want the overlapping window, set window size and stepping
--- 211,227 ----
  
  * Divide a genome sequence into sections of 10000bp and
!   output FASTA formatted sequences (line width 60 chars). The 1000bp at the
!   start and end of each subsequence overlapped. At the 3' end of the sequence
!   the leftover is also added:
  
      i = 1
+     textwidth=60
      remainder = seq.window_search(10000, 9000) do |s|
!       puts s.to_fasta("segment #{i}", textwidth)
        i += 1
      end
!     if remainder
!       puts remainder.to_fasta("segment #{i}", textwidth) 
!     end
  
  If you don't want the overlapping window, set window size and stepping
***************
*** 211,224 ****
  * Count the codon usage
  
!     codon_usage = Hash.new(0)
!     seq.window_search(3, 3) do |s|
!       codon_usage[s] += 1
!     end
  
  * Calculate molecular weight for each 10-aa peptide (or 10-nt nucleic acid)
  
!     seq.window_search(10, 10) do |s|
!       puts s.molecular_weight
!     end
  
  In most cases, sequences are read from files or retrieved from databases.
--- 232,251 ----
  * Count the codon usage
  
!   bioruby> codon_usage = Hash.new(0)
!   bioruby> seq.window_search(3, 3) do |s|
!   bioruby>   codon_usage[s] += 1
!   bioruby> end
!   bioruby> codon_usage
!   ==> {"cat"=>1, "aaa"=>3, "cca"=>1, "att"=>2, "aga"=>1, "atc"=>1, "cta"=>1, "gca"=>1, "cga"=>1, "tca"=>3, "aag"=>1, "tcc"=>1, "atg"=>1}
! 
  
  * Calculate molecular weight for each 10-aa peptide (or 10-nt nucleic acid)
  
!   bioruby> a = []
!   bioruby> seq.window_search(10, 10) do |s|
!   bioruby>   a.push s.molecular_weight
!   bioruby> end
!   bioruby> a
!   ==> [3096.2062, 3086.1962, 3056.1762, 3023.1262, 3073.2262]
  
  In most cases, sequences are read from files or retrieved from databases.
***************
*** 246,249 ****
--- 273,280 ----
      % ruby na2aa.rb my_naseq.txt
  
+ or use a pipe!
+ 
+     % cat my_naseq.txt|ruby na2aa.rb
+ 
  Outputs
  
***************
*** 254,259 ****
      % ruby -r bio -e 'p Bio::Sequence::NA.new($<.read).translate' my_naseq.txt
  
! In the next section we will retrieve data from databases instead of
! using raw sequence files.
  
  == Parsing GenBank data (Bio::GenBank class)
--- 285,291 ----
      % ruby -r bio -e 'p Bio::Sequence::NA.new($<.read).translate' my_naseq.txt
  
! In the next section we will retrieve data from databases instead of using raw
! sequence files. One generic example of the above can be found in
! ./sample/na2aa.rb.
  
  == Parsing GenBank data (Bio::GenBank class)
***************
*** 460,474 ****
  Array and BioPerl's Bio::SimpleAlign.  A very simple example is:
  
!   require 'bio'
! 
!   seqs = [ 'atgca', 'aagca', 'acgca', 'acgcg' ]
!   seqs = seqs.collect{ |x| Bio::Sequence::NA.new(x) }
! 
    # creates alignment object
!   a = Bio::Alignment.new(seqs)
! 
!   # shows consensus sequence
!   p a.consensus             # ==> "a?gc?"
! 
    # shows IUPAC consensus
    p a.consensus_iupac       # ==> "ahgcr"
--- 492,501 ----
  Array and BioPerl's Bio::SimpleAlign.  A very simple example is:
  
!   bioruby> seqs = [ 'atgca', 'aagca', 'acgca', 'acgcg' ]
!   bioruby> seqs = seqs.collect{ |x| Bio::Sequence::NA.new(x) }
    # creates alignment object
!   bioruby> a = Bio::Alignment.new(seqs)
!   bioruby> a.consensus 
!   ==> "xa?gc?"
    # shows IUPAC consensus
    p a.consensus_iupac       # ==> "ahgcr"
***************
*** 1168,1179 ****
  == The BioRuby example programs
  
! Some sample programs are stored in samples/ directry.
! Some programs are obsolete. Since samples are not enough,
! practical and interesting samples are welcome.
! 
! to be written...
  
! (EDITOR's NOTE: I would like some examples automatically
! included - with output)
  
  == Unit testing and doctests
--- 1195,1201 ----
  == The BioRuby example programs
  
! Some sample programs are stored in ./samples/ directory. Run for example:
  
!   ./sample/na2aa.rb test/data/fasta/example1.txt 
  
  == Unit testing and doctests
***************
*** 1195,1198 ****
--- 1217,1242 ----
  ((<URL:http://bioruby.org/rdoc/>)).
  
+ == BioRuby Shell
+ 
+ The BioRuby shell implementation you find in ./lib/bio/shell. It is very interesting
+ as it uses IRB (the Ruby intepreter) which is a powerful environment described in
+ ((<Programming Ruby's irb chapter|URL:http://ruby-doc.org/docs/ProgrammingRuby/html/irb.html>)). IRB commands can directly be typed in the shell, e.g.
+ 
+   bioruby!> IRB.conf[:PROMPT_MODE]
+   ==!> :PROMPT_C
+ 
+ optionally you also may want to install the optional Ruby readline support -
+ with Debian libreadline-ruby. To edit a previous line you may have to press
+ line down (arrow down) first.
+ 
+ = Helpful tools
+ 
+ Apart from rdoc you may also want to use rtags - which allows jumping around
+ source code by clicking on class and method names. 
+ 
+   cd bioruby/lib
+   rtags -R --vi
+ 
+ For a tutorial see ((<URL:http://rtags.rubyforge.org/>))
  
  = APPENDIX
***************
*** 1227,1230 ****
--- 1271,1283 ----
  carefully that come with each package.
  
+ == Trouble shooting
+ 
+ * Error: in `require': no such file to load -- bio (LoadError)
+ 
+ Ruby fails to find the BioRuby libraries - add it to the RUBYLIB path, or pass
+ it to the interpeter. For example:
+ 
+   ruby -I~/cvs/bioruby/lib yourprogram.rb
+ 
  == Modifying this page
  



From pjotr at dev.open-bio.org  Mon Feb 11 08:03:36 2008
From: pjotr at dev.open-bio.org (Pjotr Prins)
Date: Mon, 11 Feb 2008 08:03:36 -0000
Subject: [BioRuby-cvs] bioruby/doc Tutorial.rd,1.19,1.20
Message-ID: <200802110803.m1B83TYu007417@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/doc
In directory dev.open-bio.org:/tmp/cvs-serv7397

Modified Files:
	Tutorial.rd 
Log Message:
Minor adjustments to Tutorial

Index: Tutorial.rd
===================================================================
RCS file: /home/repository/bioruby/bioruby/doc/Tutorial.rd,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -d -r1.19 -r1.20
*** Tutorial.rd	11 Feb 2008 07:08:46 -0000	1.19
--- Tutorial.rd	11 Feb 2008 08:03:27 -0000	1.20
***************
*** 497,519 ****
    bioruby> a = Bio::Alignment.new(seqs)
    bioruby> a.consensus 
!   ==> "xa?gc?"
    # shows IUPAC consensus
!   p a.consensus_iupac       # ==> "ahgcr"
! 
    # iterates over each seq
    a.each { |x| p x }
!     # ==>
!     #    "atgca"
!     #    "aagca"
!     #    "acgca"
!     #    "acgcg"
    # iterates over each site
    a.each_site { |x| p x }
!     # ==>
!     #    ["a", "a", "a", "a"]
!     #    ["t", "a", "c", "c"]
!     #    ["g", "g", "g", "g"]
!     #    ["c", "c", "c", "c"]
!     #    ["a", "a", "a", "g"]
  
    # doing alignment by using CLUSTAL W.
--- 497,519 ----
    bioruby> a = Bio::Alignment.new(seqs)
    bioruby> a.consensus 
!   ==> "a?gc?"
    # shows IUPAC consensus
!   a.consensus_iupac 
!   ==> "ahgcr"
    # iterates over each seq
    a.each { |x| p x }
!   # ==>
!   #    "atgca"
!   #    "aagca"
!   #    "acgca"
!   #    "acgcg"
    # iterates over each site
    a.each_site { |x| p x }
!   # ==>
!   #    ["a", "a", "a", "a"]
!   #    ["t", "a", "c", "c"]
!   #    ["g", "g", "g", "g"]
!   #    ["c", "c", "c", "c"]
!   #    ["a", "a", "a", "g"]
  
    # doing alignment by using CLUSTAL W.



From pjotr at dev.open-bio.org  Wed Feb 13 08:04:41 2008
From: pjotr at dev.open-bio.org (Pjotr Prins)
Date: Wed, 13 Feb 2008 08:04:41 -0000
Subject: [BioRuby-cvs] bioruby/doc Tutorial.rd,1.20,1.21
Message-ID: <200802130804.m1D84XQC015600@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/doc
In directory dev.open-bio.org:/tmp/cvs-serv15580

Modified Files:
	Tutorial.rd 
Log Message:
Tutorial

Index: Tutorial.rd
===================================================================
RCS file: /home/repository/bioruby/bioruby/doc/Tutorial.rd,v
retrieving revision 1.20
retrieving revision 1.21
diff -C2 -d -r1.20 -r1.21
*** Tutorial.rd	11 Feb 2008 08:03:27 -0000	1.20
--- Tutorial.rd	13 Feb 2008 08:04:30 -0000	1.21
***************
*** 183,187 ****
  through a variable named +s+.
  
! * Show average percentage of GC content for 20 bases (stepping the default one base at a time)
  
    bioruby> seq = Bio::Sequence::NA.new("atgcatgcaattaagctaatcccaattagatcatcccgatcatcaaaaaaaaaa")
--- 183,187 ----
  through a variable named +s+.
  
! Show average percentage of GC content for 20 bases (stepping the default one base at a time)
  
    bioruby> seq = Bio::Sequence::NA.new("atgcatgcaattaagctaatcccaattagatcatcccgatcatcaaaaaaaaaa")
***************
*** 197,201 ****
  use all methods on the subsequence. For example,
  
! * Shows translation results for 15 bases shifting a codon at a time
  
    bioruby> a = []
--- 197,201 ----
  use all methods on the subsequence. For example,
  
! Shows translation results for 15 bases shifting a codon at a time
  
    bioruby> a = []
***************
*** 210,217 ****
  subsequence. This allows for example
  
! * Divide a genome sequence into sections of 10000bp and
!   output FASTA formatted sequences (line width 60 chars). The 1000bp at the
!   start and end of each subsequence overlapped. At the 3' end of the sequence
!   the leftover is also added:
  
      i = 1
--- 210,217 ----
  subsequence. This allows for example
  
! Divide a genome sequence into sections of 10000bp and
! output FASTA formatted sequences (line width 60 chars). The 1000bp at the
! start and end of each subsequence overlapped. At the 3' end of the sequence
! the leftover is also added:
  
      i = 1
***************
*** 230,234 ****
  Other examples
  
! * Count the codon usage
  
    bioruby> codon_usage = Hash.new(0)
--- 230,234 ----
  Other examples
  
! Count the codon usage
  
    bioruby> codon_usage = Hash.new(0)
***************
*** 240,244 ****
  
  
! * Calculate molecular weight for each 10-aa peptide (or 10-nt nucleic acid)
  
    bioruby> a = []
--- 240,244 ----
  
  
! Calculate molecular weight for each 10-aa peptide (or 10-nt nucleic acid)
  
    bioruby> a = []
***************
*** 399,408 ****
      end
  
! * Note: In this example Feature#assoc method makes a Hash from a
!   feature object. It is useful because you can get data from the hash
!   by using qualifiers as keys.
!   (But there is a risk some information is lost when two or more
!   qualifiers are the same. Therefore an Array is returned by
!   Feature#feature)
  
  Bio::Sequence#splicing splices subsequence from nucleic acid sequence
--- 399,408 ----
      end
  
! Note: In this example Feature#assoc method makes a Hash from a
! feature object. It is useful because you can get data from the hash
! by using qualifiers as keys.
! (But there is a risk some information is lost when two or more
! qualifiers are the same. Therefore an Array is returned by
! Feature#feature)
  
  Bio::Sequence#splicing splices subsequence from nucleic acid sequence
***************
*** 418,426 ****
  bio/location.rb.
  
! * Splice according to location string used in a GenBank entry
  
      naseq.splicing('join(2035..2050,complement(1775..1818),13..345')
  
! * Generate Bio::Locations object and pass the splicing method
  
      locs = Bio::Locations.new('join((8298.8300)..10206,1..855)')
--- 418,426 ----
  bio/location.rb.
  
! Splice according to location string used in a GenBank entry
  
      naseq.splicing('join(2035..2050,complement(1775..1818),13..345')
  
! Generate Bio::Locations object and pass the splicing method
  
      locs = Bio::Locations.new('join((8298.8300)..10206,1..855)')
***************
*** 430,434 ****
  (Bio::Sequence::AA objects).
  
! * Splicing peptide from a protein (e.g. signal peptide)
  
      aaseq.splicing('21..119')
--- 430,434 ----
  (Bio::Sequence::AA objects).
  
! Splicing peptide from a protein (e.g. signal peptide)
  
      aaseq.splicing('21..119')