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

View of /FigKernelScripts/sims_all.pl

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1.6 - (download) (as text) (annotate)
Wed Dec 17 16:19:51 2008 UTC (10 years, 11 months ago) by overbeek
Branch: MAIN
CVS Tags: mgrast_dev_08112011, rast_rel_2009_05_18, mgrast_dev_08022011, rast_rel_2014_0912, myrast_rel40, mgrast_dev_05262011, rast_rel_2008_12_18, mgrast_dev_04082011, rast_rel_2010_0928, mgrast_version_3_2, mgrast_dev_12152011, mgrast_dev_06072011, 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, rast_rel_2009_02_05, rast_rel_2011_0119, 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, mgrast_dev_04012011, rast_rel_2009_07_09, rast_rel_2010_0827, myrast_33, rast_rel_2011_0928, mgrast_dev_04052011, mgrast_dev_02222011, rast_rel_2009_03_26, mgrast_dev_10262011, HEAD
Changes since 1.5: +4 -1 lines
remove paralogs before computing conections

#
# 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;

$usage = "usage: sims_all [-no_redo_blast] Type IdenCutoff CovCutoff FastaD SimsDir Genome1 Genome2 ...";

$no_redo_blast = "";
if (@ARGV && ($ARGV[0] =~ m/^-no_redo_blast/)) {
    $no_redo_blast = shift @ARGV;
}

(
 ($type    = shift @ARGV) &&
 ($miniden = shift @ARGV) &&
 ($mincov  = shift @ARGV) &&
 ($fastaD  = shift @ARGV) &&
 ($simsD   = shift @ARGV) &&
 (@ARGV > 1)
)
    || die $usage;

@ARGV = sort { $a <=> $b } @ARGV;

&FIG::verify_dir($fastaD);
&FIG::verify_dir($simsD);

foreach $genome (@ARGV)
{
    if (! -s "$fastaD/$genome")
    {
	if ($type =~ /^p$/i)
	{
	    &FIG::run("pegs $genome | translation_of > $fastaD/$genome");
	}
	else
	{
	    &FIG::run("pegs $genome | fid2dna > $fastaD/$genome");
	}
    }
}

### Modified by RAO on Dec 17, 2008 to make it compute sims for each genome
### against itself, too

for ($i=0; ($i < @ARGV); $i++)
{
    for ($j=0; ($j < @ARGV); $j++)
    {
	if (not ($no_redo_blast && (-s "$simsD/$ARGV[$i]-$ARGV[$j]")))
	{
	    &FIG::run("sims_between $fastaD/$ARGV[$i] $fastaD/$ARGV[$j] $type $miniden $mincov > $simsD/$ARGV[$i]-$ARGV[$j]");
	}
    }
}

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3