[BioRuby-cvs] bioruby/lib/bio/db/embl embl.rb,1.29,1.29.2.1

[Jan Aerts]

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