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

View of /FigKernelScripts/db_xrefs_of.pl

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1.4 - (download) (as text) (annotate)
Mon Dec 5 18:56:37 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 1.3: +17 -0 lines
Add license words.

#
# 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;
my $fig = new FIG;

# usage: db_xrefs_of < IDs > ID-Xrefs
#

%tag_order = ( gene => 1,
	       sp   => 2,
	       nr   => 3,
	       uni  => 4,
	       kegg => 5,
	       gi   => 6,
	       fig  => 7
	     );

while (defined($line = <STDIN>))
{
    chop $line;
    if ($line =~ /(\S+)$/)
    {
	$id = $1;
	if ($id =~ /^fig\|/) 
	{
	    @possible_xrefs = ($id,$fig->feature_aliases($id));
	}
	elsif ($peg = $fig->by_alias($id))
	{
	    @possible_xrefs = ($peg,$fig->feature_aliases($peg));
	}
	else
	{
	    @possible_xrefs =  map  { $_->[0] }
	                       $fig->mapped_prot_ids($id);
	}

	@xrefs =  map { $_->[0] }        
	          grep { ($_->[1] ne "misc") && ($_->[1] ne "gene") } 
	          map { [$_,&type_alias($_)] } 
	          @possible_xrefs;
	print "$line\t",join(",",@xrefs),"\n";
    }
}

sub type_alias {
    my($alias) = @_;

    if (($alias =~ /^([^|]+)\|\S+$/) && defined($tag_order{$1}))
    {
	return $1;
    }
    elsif ($alias =~ /^[NXYZA]P_/)
    {
	return "nr";
    }
    elsif (($alias =~ /^[a-zA-Z]{3,4}$/) || ($alias =~ /^[a-zA-Z]{1,3}\d+$/))
    {
	return "gene";
    }
    return "misc";
}

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3