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Revision 1.2 - (download) (as text) (annotate)
Tue Aug 8 22:50:02 2006 UTC (13 years, 6 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 1.1: +13 -2941 lines
RAE: correcting indirect functional coupling score


# 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 strict;
use FIG;
use FIGStatisticalModels;
my $fig = new FIG;
my $fs  = new FIGStatisticalModels;

#usage: score_ifcs < ifc > scored.ifc

while (defined($_ = <STDIN>))
    my @flds = split(/\t/,$_);
    my ($peg1,$peg2,$peg3,$peg4,$bbh13,$fc34,$bbh24);
    if (@flds == 7)
	($peg1,$peg2,$peg3,$peg4,$bbh13,$fc34,$bbh24) = @flds;
	($peg1,$peg2,undef,$peg3,$peg4,$bbh13,$fc34,$bbh24) = @flds;
    my $p1 = &score_bbh($fig,$peg1,$bbh13);
    my $p2 = $fs->fc_score2probability($fc34);
    my $p3 = &score_bbh($fig,$peg4,$bbh24);
    my $sc = sprintf("%0.3f",$p1 * $p2 * $p3);
    print join("\t",($peg1,$peg2,$sc,$peg3,$peg4,$bbh13,$fc34,$bbh24)),"\n";

sub score_bbh {
    my($fig,$peg,$bsc) = @_;

    my $func = scalar($fig->function_of($peg));
    my $tc=0;
    $tc = 1 if ($func =~ /aminotransferase|system|component|oxidase|regulator|cytochrome|specific|permease|transcriptional|transport|dehydrogenase/i);

    return $fs->fc_bitscore2probability($bsc, $tc);

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