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

View of /FigKernelScripts/check_nr_and_peg_synonyms.pl

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1.2 - (download) (as text) (annotate)
Mon Dec 5 18:56:37 2005 UTC (14 years, 2 months ago) by olson
Branch: MAIN
CVS Tags: mgrast_dev_08112011, rast_rel_2009_05_18, mgrast_dev_08022011, rast_rel_2014_0912, rast_rel_2008_06_18, myrast_rel40, rast_rel_2008_06_16, mgrast_dev_05262011, rast_rel_2008_12_18, mgrast_dev_04082011, rast_rel_2008_07_21, rast_rel_2010_0928, rast_2008_0924, mgrast_version_3_2, mgrast_dev_12152011, rast_rel_2008_04_23, mgrast_dev_06072011, rast_rel_2008_09_30, rast_rel_2009_0925, rast_rel_2010_0526, rast_rel_2014_0729, mgrast_dev_02212011, rast_rel_2010_1206, caBIG-05Apr06-00, mgrast_release_3_0, mgrast_dev_03252011, rast_rel_2010_0118, mgrast_rel_2008_0924, mgrast_rel_2008_1110_v2, rast_rel_2009_02_05, rast_rel_2011_0119, mgrast_rel_2008_0625, 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, rast_rel_2008_10_09, mgrast_dev_04012011, rast_release_2008_09_29, mgrast_rel_2008_0806, mgrast_rel_2008_0923, mgrast_rel_2008_0919, rast_rel_2009_07_09, rast_rel_2010_0827, mgrast_rel_2008_1110, myrast_33, rast_rel_2011_0928, rast_rel_2008_09_29, mgrast_rel_2008_0917, rast_rel_2008_10_29, mgrast_dev_04052011, mgrast_dev_02222011, caBIG-13Feb06-00, rast_rel_2009_03_26, mgrast_dev_10262011, rast_rel_2008_11_24, rast_rel_2008_08_07, HEAD
Changes since 1.1: +17 -0 lines
Add license words.

# -*- perl -*-
#
# 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.
#


use FIG;

$usage = "check_nr_and_peg_synonyms nr_file synonyms_file";

(  ($nr  = shift @ARGV) && (-s $nr)
&& ($syn = shift @ARGV) && (-s $syn)
)  || die "usage: $usage";

open( NR, "<$nr")  || die "Could not read-open $nr";
while (($id, $seqP) = &FIG::read_fasta_record(\*NR))
{ 
    $in_nr{$id} = length($$seqP);
}
close(NR) || die "Could not close $nr";

$bad = 0;
open(SYN, "<$syn") || die "Could not read-open $syn";
while (defined($entry = <SYN>))
{
    $entry =~ m/^([^,]+),(\d+)/;
    ($id, $len) = ($1, $2);
    
    if ($in_nr{$id})
    {
	if ($len != $in_nr{$id})
	{
	    $bad = 1;
	    print "Bad synonym length:\t$id\t$in_nr{$id}\t$len\n";
	}
	
	delete $in_nr{$id};
    }
    else
    {
	$bad = 1;
	print "Bad synonym ID:\t$id\n";
    }
}


if ($bad)
{
    print STDERR "FATAL ERROR: Inconsistent $nr and $syn\n";
}
else
{
    print STDERR "Consistent $nr and $syn\n";
}

exit($bad << 8);

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3