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Revision 1.3 - (download) (as text) (annotate)
Tue Jun 13 23:32:15 2006 UTC (13 years, 9 months ago) by overbeek
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, 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, rast_rel_2009_03_26, mgrast_dev_10262011, rast_rel_2008_11_24, rast_rel_2008_08_07, HEAD
Changes since 1.2: +5 -2 lines
RAE: moving PIRSF to links

# 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.

# __perl__

# extract data from subsystems for PIR people. We want data in the format: uniprot id	peg id		subsystem name	functional role

use FIG;
use strict;
my $fig=new FIG;

#foreach my $attr ($fig->get_attributes('', 'PIRSF')) {
foreach my $tple ($fig->fids_with_link_to('PIRSF'))
 #my ($peg, $tag, $value, $url)=@$attr;
 my ($peg, $link)=@$tple;
 my @aliases = $fig->feature_aliases($peg);
 my @tmp; my $ext;
 if ((@tmp = grep { $_ =~ /^uni\|/ } @aliases) > 0) {$ext=join ",", @tmp}
 elsif ((@tmp = grep { $_ =~ /^sp\|/ } @aliases) > 0) {$ext=join ",", @tmp}
 elsif ((@tmp = grep { $_ =~ /^gi\|/ } @aliases) > 0) {$ext=join ",", @tmp}
 my $allss;
 foreach my $subsys ($fig->subsystems_for_peg($peg)) {my $spaced=$$subsys[0]; $spaced =~ s/_/ /g; $allss.=$spaced."; "} $allss =~ s/; $//;
 print join "\t", $peg, $ext, $allss, scalar $fig->function_of($peg), "\n";

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