[BioRuby-cvs] bioruby/lib/bio/db/kegg ortholog.rb,1.7,1.8
Katayama Toshiaki
k at dev.open-bio.org
Thu Apr 5 15:37:52 UTC 2007
Update of /home/repository/bioruby/bioruby/lib/bio/db/kegg
In directory dev.open-bio.org:/tmp/cvs-serv16283
Modified Files:
ortholog.rb
Log Message:
* Recently, KEGG KO database is renamed to KEGG ORTHOLOG, so we follow the change as
* ko.rb is renamed to ortholog.rb
* Bio::KEGG::KO is renamed to Bio::KEGG::ORTHOLOG
* genes and dblinks methods are rewrited to use lines_fetch
Index: ortholog.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/kegg/ortholog.rb,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** ortholog.rb 8 Mar 2007 00:20:21 -0000 1.7
--- ortholog.rb 5 Apr 2007 15:37:50 -0000 1.8
***************
*** 1,6 ****
#
! # = bio/db/kegg/ko.rb - KO (KEGG Orthology) database class
#
! # Copyright:: Copyright (C) 2003 Toshiaki Katayama <k at bioruby.org>
# Copyright:: Copyright (C) 2003 Masumi Itoh <m at bioruby.org>
#
--- 1,6 ----
#
! # = bio/db/kegg/ortholog.rb - KEGG ORTHOLOG database class
#
! # Copyright:: Copyright (C) 2003-2007 Toshiaki Katayama <k at bioruby.org>
# Copyright:: Copyright (C) 2003 Masumi Itoh <m at bioruby.org>
#
***************
*** 22,26 ****
# * ftp://ftp.genome.jp/pub/kegg/tarfiles/ko
#
! class KO < KEGGDB
DELIMITER = RS = "\n///\n"
--- 22,26 ----
# * ftp://ftp.genome.jp/pub/kegg/tarfiles/ko
#
! class ORTHOLOG < KEGGDB
DELIMITER = RS = "\n///\n"
***************
*** 70,80 ****
def dblinks
unless @data['DBLINKS']
! hash = {}
! get('DBLINKS').scan(/(\S+):\s*(.*)\n/).each do |k, v|
! hash[k] = v.split(/\s+/)
! end
! @data['DBLINKS'] = hash
end
! @data['DBLINKS'] # Hash of DB:ID in DBLINKS
end
--- 70,76 ----
def dblinks
unless @data['DBLINKS']
! @data['DBLINKS'] = lines_fetch('DBLINKS')
end
! @data['DBLINKS']
end
***************
*** 82,102 ****
def genes
unless @data['GENES']
! hash = {}
! k = ''
! get('GENES').each_line do |line|
! line.chomp!
! line[0, @tagsize] = ''
! if line =~ /(\S+):/
! k = $1
! hash[k] = []
! end
! line[0, 5] = ''
! line.gsub(/\(\S+/, '').each(' ') do |u|
! hash[k] << u.strip
! end
! end
! @data['GENES'] = hash
end
! @data['GENES'] # Hash of DB:ID in DBLINKS
end
--- 78,84 ----
def genes
unless @data['GENES']
! @data['GENES'] = lines_fetch('GENES')
end
! @data['GENES']
end
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