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#!/usr/bin/env ruby
#
# fastasort: Sorts a FASTA file (in fact it can use any flat file input supported
# by BIORUBY) while modifying the definition of each record in the
# process so it is suitable for processing with (for example) pal2nal
# and PAML.
#
# 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: fastasort.rb,v 1.2 2008/05/19 12:22:05 pjotr Exp $
#
require 'bio'
include Bio
table = Hash.new # table to sort objects
ARGV.each do | fn |
Bio::FlatFile.auto(fn).each do | item |
# Some procession of the definition for external programs (just
# an example):
# strip JALView extension from definition e.g. .../1-212
if item.definition =~ /\/\d+-\d+$/
item.definition = $`
end
# substitute slashes:
definition = item.definition.gsub(/\//,'-')
# substitute quotes and ampersands:
definition = item.definition.gsub(/['"&]/,'x')
# prefix letters if the first position is a number:
definition = 'seq'+definition if definition =~ /^\d/
# Now add the data to the sort table
table[definition] = item.data
end
end
# Output sorted table
table.sort.each do | definition, data |
rec = Bio::FastaFormat.new('> '+definition.strip+"\n"+data)
print rec
end
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