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Revision 1.3 - (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 1.2: +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 strict;
use FIG;

my $usage = "usage: process_sim_deletions_and_replacements InDir OutDir Replaced Deleted";

my($in_dir,$out_dir,$rep,$del);

(
 ($in_dir  = shift @ARGV) &&
 ($out_dir = shift @ARGV) &&
 ($rep     = shift @ARGV) && open(REP,"<$rep") &&
 ($del     = shift @ARGV) && open(DEL,"<$del")
)
    || die $usage;

my %replace_with;
while (defined($_ = <REP>))
{
    if ($_ =~ /^(\S+)\t(\S+)/)
    {
	$replace_with{$1} = $2;
    }
}
close(REP);

my %to_delete;
while (defined($_ = <DEL>))
{
    if ($_ =~ /^(\S+)/)
    {
	$to_delete{$1} = 1;
    }
}
close(DEL);

opendir(SIMS,$in_dir)
    || die "could not open $in_dir";
my @files = grep { $_ !~ /^\./ } readdir(SIMS);
closedir(SIMS);


mkdir($out_dir,0777) || die "could not make $out_dir";

my($file,$rep1,$rep2,$id1,$id2,$x);
foreach $file (@files)
{
    print STDERR "processing $file\n";
    open(OLD,"<$in_dir/$file")
        || die "could not open $in_dir/$file";

    open(NEW,">$out_dir/$file")
        || die "could not open $out_dir/$file";

    while (defined($_ = <OLD>))
    {
	if ($_ =~ /^(\S+)\t(\S+)/)
	{
	    if (! ($to_delete{$1} || $to_delete{$2}))
	    {
		$rep1 = $replace_with{$1};
		$rep2 = $replace_with{$2};
		if ((! $rep1) && (! $rep2))
		{
		    print NEW $_;
		}
		elsif ($_ -~ /^(\S+)\t(\S+)(.*)$/)
		{
		    $id1 = ($x = $replace_with{$1}) ? $x : $1;
		    $id2 = ($x = $replace_with{$2}) ? $x : $2;
		    print NEW "$id1\t$id2\t$3\n";
		}
	    }
	}
    }
    close(OLD);
    close(NEW);
}

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