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

View of /FigKernelScripts/glue_tbl_to_metabolic_reconstruction.pl

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1.1 - (download) (as text) (annotate)
Fri Dec 11 20:48:41 2009 UTC (9 years, 11 months ago) by olson
Branch: MAIN
CVS Tags: mgrast_dev_08112011, 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_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_2010_0827, myrast_33, rast_rel_2011_0928, mgrast_dev_04052011, mgrast_dev_02222011, mgrast_dev_10262011, HEAD
more anno server fixes, add some missing files

#!/usr/bin/perl -w

#
# This is a SAS Component
#

#
# 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.
#

#
# Takes two files on cmd line: metabolic reconstruction output and tab-delimlited tbl output.
# Column 2 of the reconstruction is expected to be a protein ID; append the contig/beg/end  from the tbl
# file after that column.
#

use strict;

@ARGV == 2 or die "Usage: $0 reconstruction-output tbl-output\n";

my $recon = shift;
my $tbl = shift;

open(R, "<", $recon) or die "cannot open $recon: $!";
open(T, "<", $tbl) or die "cannot open $tbl: $!";

my %tbl;
while (<T>)
{
    chomp;
    my(@a) = split(/\t/);
    $tbl{$a[0]} = [@a];
}
close(T);

while (<R>)
{
    chomp;
    my(@a) = split(/\t/);
    my $l = $tbl{$a[1]};
    if ($l)
    {
	splice(@a, 1, 1, @$l);
    }
    print join("\t", @a), "\n";
}

close(R);
    

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3