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Revision 1.2 - (download) (as text) (annotate)
Mon Dec 5 18:56:38 2005 UTC (13 years, 11 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.
#


# usage: to_gids < FileOfFIGids > 4-column table
#
#       writes out tab-separated [FIGid,GIid,FIGfunction,GIfunction]

use FIG;
my $fig = new FIG;

@ids = map { $_ =~ /^(\S+)/; $1 } <STDIN>;

foreach $peg (@ids)
{
    $peg_func = $fig->function_of($peg);
    @aliases = $fig->feature_aliases($peg);
    $gi = &find_match($peg,\@aliases,"gi");
    $gi_func = ($gi eq "NA") ? "NA" : scalar $fig->function_of($gi);
    print join("\t",($peg,$gi,$peg_func,$gi_func)),"\n";
}
sub find_match {
    my($peg,$aliases,$who) = @_;
    my @hits;

    my $x = "NA";

    my @tmp = grep { $_ =~ /^$who/ } @$aliases;
    if (@tmp == 1)
    {
	$x = $tmp[0];
    }
    else
    {
	$maj = $fig->maps_to_id($peg);
	@hits = grep { $_ =~ /^$who/ } map { $_->[0] } $fig->mapped_prot_ids($peg);
	if (@hits == 1)
	{
	    $x = $hits[0];
	}
    }
    return $x;
}

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