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Revision 1.1 - (download) (as text) (annotate)
Mon Jan 14 22:14:55 2013 UTC (6 years, 10 months ago) by overbeek
Branch: MAIN
gets genomes needed to derive kmers

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;
	    my $md5 = $fig->genome_md5sum($genome);
	    if ((! $seen{$md5}) && $fig->is_prokaryotic($genome))
	    {
		$seen{$md5} = 1;
		print $_;
	    }
	}
    }
}


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