[Bio] / FigKernelScripts / bbhs.pl Repository:
ViewVC logotype

View of /FigKernelScripts/bbhs.pl

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1.7 - (download) (as text) (annotate)
Mon Dec 5 18:56:37 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 1.6: +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;

my $usage = "usage: bbhs [CutOff] [iterate] < PEG > PEG1-Sc-PEG";

my($cutoff,$pair,$peg);

my $iterate = 0;
my $i;
for ($i=0; ($i < @ARGV) && ($ARGV[$i] !~ /iterate/i); $i++) {}
if ($i < @ARGV)
{
    $iterate = 1;
    splice(@ARGV,$i,1);
}

$cutoff = shift @ARGV;
$cutoff = defined($cutoff) ? $cutoff : 1.0e-10;

my $id;
@pegs = map { chop; $_ =~ /(\S+)$/; 
	      $id = $1;  
	      if ($id =~ /^fig\|/)
	      {
		  $id;
	      }
	      else
	      {
		  if ($peg = $fig->by_alias($id))
		  {
		      $peg;
		  }
		  else
		  {
		      ();
		  }
	      }
            } <STDIN>;

%pegs = map { $_ => 1 } @pegs;

my @to_process = keys(%pegs);
my %seenG = map { ("$_," . &FIG::genome_of($_) ) => 1 } @to_process;
my %from  = map { $_ => $_ } @to_process;
my %seenP = map { $_ => 1 } @to_process;

my $i;
for ($i=0; ($i < @to_process); $i++)
{
    $peg = $to_process[$i];

    foreach $pair ($fig->bbhs($peg,$cutoff))
    {
	($peg1,$sc) = @$pair;
	if ((! $seenP{$peg1}) && (! $seenG{$from{$peg} . "," . &FIG::genome_of($peg1)}))
	{
	    $seenP{$peg1} = 1;
	    $from{$peg1} = $from{$peg};
	    $seenG{$from{$peg} . "," . &FIG::genome_of($peg1)} = 1;

	    push(@hits,[$peg,$sc,$peg1]);
	    if ($iterate)
	    {
		push(@to_process,$peg1);
	    }
	}
    }
}

foreach $x (sort { $a->[1] <=> $b->[1] } @hits)
{
    print join("\t",@$x),"\n";
}

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3