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#!/usr/bin/env ruby
#
# gt2fasta.rb - convert GenBank translations into FASTA format (pep)
#
# Copyright (C) 2001 KATAYAMA Toshiaki <k@bioruby.org>
#
# 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: gt2fasta.rb,v 0.3 2002/04/15 03:06:17 k Exp $
#
require 'bio/io/flatfile'
require 'bio/feature'
require 'bio/db/genbank'
include Bio
ff = FlatFile.new(GenBank, ARGF)
while gb = ff.next_entry
orf = 0
gb.features.each do |f|
f = f.assoc
if aaseq = f['translation']
orf += 1
gene = [
f['gene'],
f['product'],
f['note'],
f['function']
].compact.join(', ')
definition = "gp:#{gb.entry_id}_#{orf} #{gene} [#{gb.organism}]"
print aaseq.to_fasta(definition, 70)
end
end
end
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