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Revision 1.2 - (download) (as text) (annotate)
Mon Dec 5 18:56:38 2005 UTC (14 years, 2 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.

#
# 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 = "usage: project FileOfPegs Genome";

(
 ($pegsF  = shift @ARGV) &&
 ($genome = shift @ARGV)
)
    || die $usage;

$genomeQ = quotemeta $genome;
@pegs = map { ($_ =~ /^(fig\|\d+\.\d+\.peg\.\d+)/) ? $1 : () } `cat $pegsF`;


foreach $peg (@pegs)
{
    $genome1 = &FIG::genome_of($peg);
    $genome1Q = quotemeta $genome1;

    print join("\t",($peg,scalar $fig->function_of($peg))), "\n";
    @bbhs = grep { $_->[0] =~ /fig\|$genomeQ\.peg/ } $fig->bbhs($peg,10000);
    if (@bbhs > 0)
    {
	if (@bbhs > 1)
	{
	    print STDERR &Dumper(\@bbhs);
	    die "BAD BBHs";
	}
	print "\tBBH:$bbhs[0]->[0]\t$bbhs[0]->[1]\n\n";
    }
	
    @sims1 = map { [$_->id2,$_->psc] } grep { $_->id2 =~ /fig\|$genomeQ\.peg/ } $fig->sims($peg,10000,1.0e-5,"fig");
    if (@sims1 > 0)
    {
	if (@sims1 > 5) { $#sims1 = 4 }
	foreach $sim1 (@sims1)
	{
	    ($id1,$psc1) = @$sim1;
	    $func1 = $fig->function_of($id1);
	    print "\t$psc1\t$id1\t$func1\n";

	    @bbhs = grep { $_->[0] =~ /fig\|$genome1Q\.peg/ } $fig->bbhs($id1,10000);
	    if (@bbhs > 0)
	    {
		if (@bbhs > 1)
		{
		    print STDERR &Dumper(\@bbhs);
		    die "BAD BBHs";
		}
		print "\t\tBBH:$bbhs[0]->[0]\t$bbhs[0]->[1]\n\n";
	    }
	

	    @sims2 = map { [$_->id2,$_->psc] } grep { $_->id2 =~ /fig\|$genome1Q\.peg/ } $fig->sims($id1,10000,1.0e-5,"fig");
	    if (@sims2 > 5) { $#sims2 = 4 }
	    foreach $sim2 (@sims2)
	    {
		($id2,$psc2) = @$sim2;
		$func2 = $fig->function_of($id2);
		print "\t\t$psc2\t$id2\t$func2\n";
	    }
	}
    }
}


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