[BioRuby-cvs] bioruby/lib/bio/db/genbank genbank.rb,0.38,0.39
Katayama Toshiaki
k at dev.open-bio.org
Tue Sep 19 05:59:09 UTC 2006
Update of /home/repository/bioruby/bioruby/lib/bio/db/genbank
In directory dev.open-bio.org:/tmp/cvs-serv32155/lib/bio/db/genbank
Modified Files:
genbank.rb
Log Message:
* license is changed from LGPL to Ruby's
* document is changed to RDoc
Index: genbank.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/genbank/genbank.rb,v
retrieving revision 0.38
retrieving revision 0.39
diff -C2 -d -r0.38 -r0.39
*** genbank.rb 7 Dec 2005 11:23:51 -0000 0.38
--- genbank.rb 19 Sep 2006 05:59:07 -0000 0.39
***************
*** 1,22 ****
#
! # bio/db/genbank/genbank.rb - GenBank database class
! #
! # Copyright (C) 2000-2005 KATAYAMA Toshiaki <k at bioruby.org>
! #
! # This library is free software; you can redistribute it and/or
! # modify it under the terms of the GNU Lesser General Public
! # License as published by the Free Software Foundation; either
! # version 2 of the License, or (at your option) any later version.
! #
! # This library 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
! # Lesser General Public License for more details.
#
! # You should have received a copy of the GNU Lesser General Public
! # License along with this library; if not, write to the Free Software
! # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
! # $Id$
#
--- 1,9 ----
#
! # = bio/db/genbank/genbank.rb - GenBank database class
#
! # Copyright:: Copyright (C) 2000-2005 Toshiaki Katayama <k at bioruby.org>
! # License:: Ruby's
#
! # $Id$
#
***************
*** 25,33 ****
module Bio
class GenBank < NCBIDB
include Bio::NCBIDB::Common
! # LOCUS
class Locus
def initialize(locus_line)
--- 12,32 ----
module Bio
+
+ # == Description
+ #
+ # Parses a GenBank formatted database entry
+ #
+ # == Example
+ #
+ # # entry is a string containing only one entry contents
+ # gb = Bio::GenBank.new(entry)
+ #
class GenBank < NCBIDB
include Bio::NCBIDB::Common
! # Parses the LOCUS line and returns contents of the LOCUS record
! # as a Bio::GenBank::Locus object. Locus object is created automatically
! # when Bio::GenBank#locus, entry_id etc. methods are called.
class Locus
def initialize(locus_line)
***************
*** 56,88 ****
end
def locus
@data['LOCUS'] ||= Locus.new(get('LOCUS'))
end
- def entry_id; locus.entry_id; end
- def length; locus.length; end
- def circular; locus.circular; end
- def division; locus.division; end
- def date; locus.date; end
-
- def strand; locus.strand; end
- def natype; locus.natype; end
! # ORIGIN
! def seq
! unless @data['SEQUENCE']
! origin
! end
! Bio::Sequence::NA.new(@data['SEQUENCE'])
! end
! alias naseq seq
! alias nalen length
!
! def seq_len
! seq.length
! end
! # FEATURES
def each_cds
features.each do |feature|
--- 55,75 ----
end
+ # Accessor methods for the contents of the LOCUS record.
+
def locus
@data['LOCUS'] ||= Locus.new(get('LOCUS'))
end
+ def entry_id; locus.entry_id; end
+ def length; locus.length; end
+ def circular; locus.circular; end
+ def division; locus.division; end
+ def date; locus.date; end
! def strand; locus.strand; end
! def natype; locus.natype; end
! # FEATURES -- Iterate only for the 'CDS' portion of the Bio::Features.
def each_cds
features.each do |feature|
***************
*** 93,96 ****
--- 80,84 ----
end
+ # FEATURES -- Iterate only for the 'gene' portion of the Bio::Features.
def each_gene
features.each do |feature|
***************
*** 102,106 ****
! # BASE COUNT : obsoleted after GenBank release 138.0
def basecount(base = nil)
unless @data['BASE COUNT']
--- 90,97 ----
! # BASE COUNT (this field is obsoleted after GenBank release 138.0) --
! # Returns the BASE COUNT as a Hash. When the base is specified, returns
! # count of the base as a Fixnum. The base can be one of 'a', 't', 'g',
! # 'c', and 'o' (others).
def basecount(base = nil)
unless @data['BASE COUNT']
***************
*** 120,123 ****
--- 111,129 ----
end
+ # ORIGIN -- Returns DNA sequence in the ORIGIN record as a
+ # Bio::Sequence::NA object.
+ def seq
+ unless @data['SEQUENCE']
+ origin
+ end
+ Bio::Sequence::NA.new(@data['SEQUENCE'])
+ end
+ alias naseq seq
+ alias nalen length
+
+ def seq_len
+ seq.length
+ end
+
end # GenBank
end # Bio
***************
*** 207,354 ****
- =begin
-
- = Bio::GenBank
-
- === Initialize
-
- --- Bio::GenBank.new(entry)
-
- === LOCUS
-
- --- Bio::GenBank#locus -> Bio::Locus
-
- Returns contents of the LOCUS record as a Bio::GenBank::Locus object.
-
- --- Bio::GenBank#entry_id -> String
- --- Bio::GenBank#nalen -> Fixnum
- --- Bio::GenBank#strand -> String
- --- Bio::GenBank#natype -> String
- --- Bio::GenBank#circular -> String
- --- Bio::GenBank#division -> String
- --- Bio::GenBank#date -> String
-
- Access methods for the contents of the LOCUS record.
-
- === DEFINITION
-
- --- Bio::GenBank#definition -> String
-
- Returns contents of the DEFINITION record as a String.
-
- === ACCESSION
-
- --- Bio::GenBank#accessions -> Array
-
- Returns contents of the ACCESSION record as an Array.
-
- === VERSION
-
- --- Bio::GenBank#versions -> Array
-
- Returns contents of the VERSION record as an Array of Strings.
-
- --- Bio::GenBank#acc_version -> String
- --- Bio::GenBank#accession -> String
- --- Bio::GenBank#version -> Fixnum
- --- Bio::GenBank#gi -> String
-
- Access methods for the contents of the VERSION record.
-
- The 'acc_version' method returns the first part of the VERSION record
- as a "ACCESSION.VERSION" String, 'accession' method returns the ACCESSION
- part of the acc_version, 'version' method returns the VERSION part of the
- acc_version as a Fixnum, and the 'gi' method returns the second part of
- the VERSION record as a "GI:#######" String.
-
- === NID
-
- --- Bio::GenBank#nid -> String
-
- Returns contents of the NID record as a String.
-
- === KEYWORDS
-
- --- Bio::GenBank#keywords -> Array
-
- Returns contents of the KEYWORDS record as an Array of Strings.
-
- === SEGMENT
-
- --- Bio::GenBank#segment -> String
-
- Returns contents of the SEGMENT record as a "m/n" form String.
-
- === SOURCE
-
- --- Bio::GenBank#source -> Hash
-
- Returns contents of the SOURCE record as a Hash.
-
- --- Bio::GenBank#common_name -> String
- --- Bio::GenBank#vernacular_name -> String
- --- Bio::GenBank#organism -> String
- --- Bio::GenBank#taxonomy -> String
-
- Access methods for the contents of the SOURCE record.
-
- The 'common_name' method is same as source['common_name'].
- The 'vernacular_name' method is an alias for the 'common_name'.
- The 'organism' method is same as source['organism'].
- The 'taxonomy' method is same as source['taxonomy'].
-
- === REFERENCE
-
- --- Bio::GenBank#references -> Array
-
- Returns contents of the REFERENCE records as an Array of Bio::Reference
- objects.
-
- === COMMENT
-
- --- Bio::GenBank#comment -> String
-
- Returns contents of the COMMENT record as a String.
-
- === FEATURES
-
- --- Bio::GenBank#features -> Bio::Features
-
- Returns contents of the FEATURES record as a Bio::Features object.
-
- --- Bio::GenBank#each_cds -> Array
-
- Iterate only for the 'CDS' portion of the Bio::Features.
-
- --- Bio::GenBank#each_gene -> Array
-
- Iterate only for the 'gene' portion of the Bio::Features.
-
- === BASE COUNT
-
- --- Bio::GenBank#basecount(base = nil) -> Hash or Fixnum
-
- Returns the BASE COUNT as a Hash. When the base is specified, returns
- count of the base as a Fixnum. The base can be one of 'a', 't', 'g',
- 'c', and 'o' (others).
-
- === ORIGIN
-
- --- Bio::GenBank#origin -> String
-
- Returns contents of the ORIGIN record as a String.
-
- --- Bio::GenBank#naseq -> Bio::Sequence::NA
- --- Bio::GenBank#seq -> Bio::Sequence::NA
-
- Returns DNA sequence in the ORIGIN record as a Bio::Sequence::NA object.
-
- == SEE ALSO
-
- * ((<URL:ftp://ftp.ncbi.nih.gov/genbank/gbrel.txt>))
- * ((<URL:http://www.ncbi.nlm.nih.gov/collab/FT/index.html>))
-
- =end
-
-
--- 213,215 ----
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