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Revision 1.2 - (download) (as text) (annotate)
Mon Dec 5 18:56:37 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.
#


use Data::Dumper;
use Carp;

# usage: best_hits Id Ali
#
($id  = shift @ARGV) || die "usage: best_hits Id Ali";
($ali = shift @ARGV) || die "usage: best_hits Id Ali";

open(TMP,"<$ali") || die "usage: best_hits Id Ali";
while (defined($_ = <TMP>) && ($_ !~ /^>$id/)) {}
if ($_)
{
    @lines = ();
    while (defined($_ = <TMP>) && ($_ !~ /^>/))
    {
	$_ =~ s/\s//g;
	push(@lines,$_);
    }
    $seq = join("",@lines);
    close(TMP);

    open(TMP,">tmp$$") || die "could not open tmp$$";
    print TMP ">$id\n$seq\n";
    close(TMP);

#   @best = `SeqFortran/simrank -b $base.bin -i tmp$$ -a $base.gb -simple`;
    if (-s "$ali.bin")
    {
	@best = `simrank_nuc --query tmp$$ --data $ali --binary $ali.bin 2> /dev/null`;
    }
    else
    {
	@best = `simrank_nuc --query tmp$$ --data $ali --binary $ali.bin --rebuild 2> /dev/null`;
    }

    if ($best[$#best] =~ /^$id\s+(\S.*\S)\s*$/)
    {
	@hits = split(/\t/,$1);
	foreach $hit (@hits)
	{
	    if (($hit =~ /^(\S+):(\S+)/) && ($id1 = $1) && ($id1 ne $id))
	    {
		print "$id1\n";
	    }
	}
    }
    else
    {
	print STDERR "could not find neighbors for $id\n";
    }
    unlink("tmp$$");
}

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