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Revision 1.2 - (download) (as text) (annotate)
Mon Dec 5 18:56:38 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 1.1: +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.
#


# usage: where_does_seq_hit OrgAbbr < seq  [NOT FASTA - JUST one line of seq]

use FIG;
my $fig = new FIG;

if (@ARGV > 0)
{
    @orgs = map { $_ =~ /^(\S+)/; $1 } `cat $ARGV[0]`;
}
else
{
    @orgs = map { $_ =~ /^(\S+)/; $1 } `fig genomes complete | grep 'Staphylococcus aureus`;
}
$_ = <STDIN>;
if ($_ =~ /^(\S+)/)
{
    $dna = $1;
    foreach $org (@orgs)
    {
	my @hit = &get_loc($fig,$org,$dna);
	if (@hit)
	{
	    print "$org\t",join("\t",@hit),"\n";
	}
    }
}

sub get_loc
{
    my($fig,$org,$dna) = @_;

    open(TMP,">tmp$$") || die "tmp$$";
    print TMP ">oligo\n$dna\n";
    close(TMP);
    
    &FIG::run("formatdb -i $FIG_Config::organisms/$org/contigs -p F");
    my @hits = `blastall -i tmp$$ -d $FIG_Config::organisms/$org/contigs -m 8 -FF -e 1.0e-10 -p blastn -m 8`;
    if (@hits > 0)
    {
	@flds = split(/\t/,$hits[0]);
	if ($flds[2] >= 97.0)
	{
	    return ($flds[1],$flds[8],$flds[9],abs($flds[9]-$flds[8])+1);
	}
    }
    return undef;
}

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