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Revision 1.2 - (download) (as text) (annotate)
Fri Jul 7 19:46:48 2006 UTC (13 years, 4 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: +6 -12 lines
fixes to wseekly statistics

########################################################################
#
# 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;
use Assignments;

$usage = "usage: make_close_strain_family_tabs Sets families.tab functions.tab Prefix";

(
 ($setsF   = shift @ARGV) &&
 ($pre     = shift @ARGV)
)
    || die $usage;

open(SETS,"<$setsF")
    || die "could not open $setsF";

$n = 1;
my $parms = &Assignments::load_parms();

while (defined($_ = <SETS>))
{
    chop;
    @pegs = split(/\t/,$_);
    undef %funcs;
    foreach $peg (@pegs)
    {
	$funcs{scalar $fig->function_of($peg)} = 1;
    }
    @funcs = keys(%funcs);
    $best_function = "";

    if (@funcs > 1)
    {
	($pegs,$external_ids) = &Assignments::equivalent_ids($fig,$parms,\@pegs);
	$best_function = &Assignments::choose_best_assignment($fig,$parms,$pegs,$external_ids);
    }
    elsif (@funcs == 1)
    {
	$best_function = $funcs[0];
    }
	
    $fam = $pre . $n;
    foreach $peg (@pegs)
    {
	print join("\t",($fam,$peg,scalar $fig->function_of($peg))),"\n";
    }
    $n++;
}

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