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#!/usr/bin/env ruby
#
# fastagrep: Greps a FASTA file (in fact it can use any flat file input supported
# by BIORUBY) and outputs sorted FASTA
#
# Copyright (C) 2008 KATAYAMA Toshiaki <k@bioruby.org> & Pjotr Prins
#
# 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: fastagrep.rb,v 1.1 2008/05/19 12:22:05 pjotr Exp $
#
require 'bio'
include Bio
usage = <<USAGE
Usage: fastagrep.rb [--skip] [regex] infiles
-v Invert the sense of matching, to select non-matching lines.
Examples:
Output all sequence descriptors containing 'Arabidopsis' or 'Drosophila'
regardless of case
fastagrep.rb "/Arabidopsis|Drosophila/i" *.seq > reduced.fasta
As the result is a FASTA stream you could pipe it for sorting:
fastagrep.rb "/Arabidopsis|Drosophila/i" *.seq | fastasort.rb
USAGE
if ARGV.size == 0
print usage
exit 1
end
skip = (ARGV[0] == '-v')
ARGV.shift if skip
# ---- Valid regular expression - if it is not a file
regex = ARGV[0]
if regex=~/^\// and !File.exist?(regex)
ARGV.shift
else
print usage
exit 1
end
ARGV.each do | fn |
Bio::FlatFile.auto(fn).each do | item |
if skip
next if eval("item.definition =~ #{regex}")
else
next if eval("item.definition !~ #{regex}")
end
rec = Bio::FastaFormat.new('> '+item.definition.strip+"\n"+item.data)
print rec
end
end
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