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revision 1.2, Fri Oct 23 19:16:20 2009 UTC revision 1.3, Wed Mar 31 18:23:02 2010 UTC
# Line 5  Line 5 
5  use SeedUtils;  use SeedUtils;
6    
7  my $sapObject = SAPserver->new();  my $sapObject = SAPserver->new();
 my $coObject = COserver->new();  
8    
9  my $genomeHash = $sapObject->all_genomes(-complete => 1);  my $genomeHash = $sapObject->all_genomes(-complete => 1);
10  for my $genome (keys %$genomeHash) {  for my $genome (keys %$genomeHash) {
# Line 13  Line 12 
12      my $geneHash = $sapObject->feature_assignments(-genome => $genome,      my $geneHash = $sapObject->feature_assignments(-genome => $genome,
13                                                     -type => 'peg');                                                     -type => 'peg');
14      my @hypotheticalGenes = grep { &SeedUtils::hypo($geneHash->{$_}) } sort keys %$geneHash;      my @hypotheticalGenes = grep { &SeedUtils::hypo($geneHash->{$_}) } sort keys %$geneHash;
15      my $couplingHash = $coObject->conserved_in_neighborhood(-ids => \@hypotheticalGenes,      my $couplingHash = $sapObject->conserved_in_neighborhood(-ids => \@hypotheticalGenes,
16                                                              -hash => 1);                                                              -hash => 1);
17      for my $gene (@hypotheticalGenes) {      for my $gene (@hypotheticalGenes) {
18          my $couplingList = $couplingHash->{$gene};          my $couplingList = $couplingHash->{$gene};

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