[Bio] / FigKernelScripts / extract_DNA_for_whole_ORFs.pl Repository:
ViewVC logotype

View of /FigKernelScripts/extract_DNA_for_whole_ORFs.pl

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1.4 - (download) (as text) (annotate)
Fri Apr 17 17:51:13 2009 UTC (10 years, 10 months ago) by gdpusch
Branch: MAIN
CVS Tags: mgrast_dev_08112011, rast_rel_2009_05_18, mgrast_dev_08022011, rast_rel_2014_0912, myrast_rel40, mgrast_dev_05262011, mgrast_dev_04082011, rast_rel_2010_0928, mgrast_version_3_2, mgrast_dev_12152011, mgrast_dev_06072011, rast_rel_2009_0925, rast_rel_2010_0526, rast_rel_2014_0729, mgrast_dev_02212011, rast_rel_2010_1206, mgrast_release_3_0, mgrast_dev_03252011, rast_rel_2010_0118, rast_rel_2011_0119, mgrast_release_3_0_4, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_1, mgrast_dev_03312011, mgrast_release_3_1_2, mgrast_release_3_1_1, mgrast_release_3_1_0, mgrast_dev_04132011, mgrast_dev_04012011, rast_rel_2009_07_09, rast_rel_2010_0827, myrast_33, rast_rel_2011_0928, mgrast_dev_04052011, mgrast_dev_02222011, mgrast_dev_10262011, HEAD
Changes since 1.3: +9 -6 lines
Fixed possible DNA case sensitivity.

#
# Copyright (c) 2003-2006 University of Chicago and Fellowship
# for Interpretations of Genomes. All Rights Reserved.
#
# This file is part of the SEED Toolkit.
# 
# The SEED Toolkit is free software. You can redistribute
# it and/or modify it under the terms of the SEED Toolkit
# Public License. 
#
# You should have received a copy of the SEED Toolkit Public License
# along with this program; if not write to the University of Chicago
# at info@ci.uchicago.edu or the Fellowship for Interpretation of
# Genomes at veronika@thefig.info or download a copy from
# http://www.theseed.org/LICENSE.TXT.
#

# usage: extract_DNA_for_whole_ORFs < stream_of_ORF_objects > DNA.fasta

$/ = "///\n";
while (defined($obj = <STDIN>))
{
    chomp $obj;
    if ($obj =~ /^(.*?)\/\//so)
    {
	$obj = $1;
    }

    undef %key_value_pairs;
    foreach $kv (split(/\n/o,$obj))
    {
	if ($kv =~ /^([^=]+)=(.*)$/o)
	{
	    $key_value_pairs{$1} = $2;
	}
    }
    
    ($id  = $key_value_pairs{"ID"})       || die "missing ID";
    
    ($seq = $key_value_pairs{"SEQ"})      || die "missing SEQ";
    ($pre = $key_value_pairs{"PREFIX"})   || die "missing PREFIX";
    $seq = $pre . $seq;
    $seq = uc($seq);
    $seq =~ s/(TAA|TAG|TGA)$//o;
    
    print ">$id\n$seq\n";
}

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3