Sha256: 2b781b7bdf098238d5fe0772f5cabeae4130d09755ba1c8f9fa05d9cd9338a32
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Versions: 33
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Contents
#!/usr/bin/env ruby
#
# any2fasta.rb - convert input file into FASTA format using a regex
# filter
#
# Copyright (C) 2006 Pjotr Prins <p@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: any2fasta.rb,v 1.1 2006/02/17 14:59:27 pjotr Exp $
#
require 'bio/io/flatfile'
include Bio
usage = <<USAGE
Usage: any2fasta.rb [regex] infiles
Examples:
Output all sequences containing GATC or GATT ignoring case:
any2fasta.rb "/GAT[CT]/i" *.seq > reduced.fasta
USAGE
if ARGV.size == 0
print usage
exit 1
end
# ---- Valid regular expression - if it is not a file
regex = ARGV[0]
if regex=~/^\// and !File.exist?(regex)
ARGV.shift
else
regex = nil
end
ARGV.each do | fn |
ff = Bio::FlatFile.auto(fn)
ff.each_entry do |entry|
if regex != nil
next if eval("entry.seq !~ #{regex}")
end
print entry.seq.to_fasta(entry.definition,70)
end
end
Version data entries
33 entries across 33 versions & 4 rubygems