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Revision 1.3 - (download) (as text) (annotate)
Mon Apr 29 19:58:58 2013 UTC (6 years, 5 months ago) by overbeek
Branch: MAIN
CVS Tags: HEAD
Changes since 1.2: +1 -1 lines
fixes to pattern

use strict;
use Data::Dumper;
use FIG;
my $fig = new FIG;
use SeedEnv;

my %seen;
foreach $_ (`svr_all_genomes`)
{
    if (($_ !~ /[pP]hage\b/) && ($_ !~ /[pP]lasmid\b/))
    {
	if (($_ =~ /^(\S+)\s(\S+).*\s(\d+\.\d+)$/) && ($2 ne "sp."))
	{
	    my $genus = $1;
	    my $species = $2;
	    my $genome = $3;
	    if ($species !~ /^sp\.?$/i)
	    {
		my $md5 = $fig->genome_md5sum($genome);
		if ((! $seen{$md5}) && $fig->is_prokaryotic($genome))
		{
		    $seen{$md5} = 1;
		    print $_;
		}
	    }
	}
    }
}


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