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Annotation of /Kmers2/get_genomes_for_kmer_analysis.pl

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1 : overbeek 1.1 use strict;
2 :     use Data::Dumper;
3 :     use FIG;
4 :     my $fig = new FIG;
5 :     use SeedEnv;
6 :    
7 :     my %seen;
8 :     foreach $_ (`svr_all_genomes`)
9 :     {
10 : overbeek 1.3 if (($_ !~ /[pP]hage\b/) && ($_ !~ /[pP]lasmid\b/))
11 : overbeek 1.1 {
12 :     if (($_ =~ /^(\S+)\s(\S+).*\s(\d+\.\d+)$/) && ($2 ne "sp."))
13 :     {
14 :     my $genus = $1;
15 :     my $species = $2;
16 :     my $genome = $3;
17 : overbeek 1.2 if ($species !~ /^sp\.?$/i)
18 : overbeek 1.1 {
19 : overbeek 1.2 my $md5 = $fig->genome_md5sum($genome);
20 :     if ((! $seen{$md5}) && $fig->is_prokaryotic($genome))
21 :     {
22 :     $seen{$md5} = 1;
23 :     print $_;
24 :     }
25 : overbeek 1.1 }
26 :     }
27 :     }
28 :     }
29 :    

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