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revision 1.1, Wed Oct 21 18:17:16 2009 UTC revision 1.2, Fri Oct 23 19:16:20 2009 UTC
# Line 2  Line 2 
2  use strict;  use strict;
3  use SAPserver;  use SAPserver;
4  use COserver;  use COserver;
5    use SeedUtils;
6    
7  my $sapObject = SAPserver->new();  my $sapObject = SAPserver->new();
8  my $coObject = COserver->new();  my $coObject = COserver->new();
# Line 10  Line 11 
11  for my $genome (keys %$genomeHash) {  for my $genome (keys %$genomeHash) {
12      my $genomeName = $genomeHash->{$genome};      my $genomeName = $genomeHash->{$genome};
13      my $geneHash = $sapObject->feature_assignments(-genome => $genome,      my $geneHash = $sapObject->feature_assignments(-genome => $genome,
14                                                     -type => 'peg',                                                     -type => 'peg');
15                                                     -hypothetical => 1);      my @hypotheticalGenes = grep { &SeedUtils::hypo($geneHash->{$_}) } sort keys %$geneHash;
     my @hypotheticalGenes = sort keys %$geneHash;  
16      my $couplingHash = $coObject->conserved_in_neighborhood(-ids => \@hypotheticalGenes,      my $couplingHash = $coObject->conserved_in_neighborhood(-ids => \@hypotheticalGenes,
17                                                              -hash => 1);                                                              -hash => 1);
18      for my $gene (@hypotheticalGenes) {      for my $gene (@hypotheticalGenes) {

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