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Revision 1.1 - (download) (as text) (annotate)
Fri Dec 23 19:27:26 2005 UTC (14 years, 3 months ago) by overbeek
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
fixes to extract_genomes

# usage: same_subsys Subsystems < tuples > same 2> not_same

use FIG;
my $fig = new FIG;

($subsystems = shift @ARGV) 
    || die "usage: same_subsys Subsystems < tuples > same 2> not_same";

%all = map { $_ =~ /^(\S.*\S)/; $1 => 1 } `cat $subsystems`;

$/ = "//\n";
my @rel = map { chomp; $_ } <DATA>;
$/ = "\n";

foreach $_ (@rel)
{
    ($s1,$s2) = split(/\n/,$_);
    $rel{$s1}->{$s2} = 1;
    $rel{$s2}->{$s1} = 1;
}
while (defined($_ = <STDIN>))
{
    if (($_ =~ /^(\S+)\t(\S+)/) && &same($1,$2))
    {
	print $_;
    }
    else
    {
	print STDERR $_;
    }
}

sub same {
    my($peg1,$peg2) = @_;
    my($i,$j,$same);

    my @s1 = grep { $all{$_} } $fig->peg_to_subsystems($peg1);
    my @s2 = grep { $all{$_} } $fig->peg_to_subsystems($peg2);
    for ($i=0,$same=0; (! $same) && ($i < @s1); $i++)
    {
	for ($j=0; (! $same) && ($j < @s2); $j++)
	{
	    if (($s1[$i] eq $s2[$j]) ||
		$rel{$s1[$i]}->{$s2[$j]})
	    {
		$same = 1;
	    }
	}
    }
    return $same;
}

__DATA__
Ribosome_LSU_bacterial
Ribosome_SSU_bacterial
//

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