[ensembl-dev] Affymetrix Probesets

[Alex Kalderimis]

Dear Listizens, 

In trying to debug why code for getting Affymetrix Probeset
information had stopped working, I added some debug statements and it
seems that the data is no longer modelled as we expected it to be. The
code is below:

 69  for my $slice (@slices) {
 70  my @genes = @{ $slice->get_all_Genes };
 71  $self->debug("Processing " . scalar(@genes) . " genes");
 72  my $processed_genes = 0;
 73  for my $gene (@genes) {
 74      my @transcripts = @{ $gene->get_all_Transcripts };
 75      for my $transcript (@transcripts) {
 76          my @xrefs = @{ $transcript->get_all_DBEntries };
 77          for my $xref (@xrefs) {
 78              $xref_types{$xref->dbname} = 1;
 79              if ( $xref->dbname eq $db_name ) {
 80                  my @probe_features = @{ $self->get_feature_adaptor->fetch_all_by_probeset( $xref->display_id ) };
 81                  for my $probe_feature (@probe_features) {
 82                      my $line = join("\t",
 83                          $gene->stable_id,
 84                          $transcript->stable_id,
 85                          $xref->display_id,
 86                          $probe_feature->seq_region_name,
 87                          $probe_feature->seq_region_start,
 88                          $probe_feature->seq_region_end);
 89                      $self->debug($line);
 90                      print $out $line, "\n";
 91                  }
 92              }
 93          }
 94      }
 95      $processed_genes++;
 96      if ($processed_genes % 100 == 0) {
 97          $self->debug("Processed $processed_genes genes, with the following XREF types: " . join(", ", sort keys %xref_types));
 98      }
 99  }

The dbnames "AFFY_Drosophila_1" and "AFFY_Drosphila_2" (which are what I 
am looking for) never appear. How can I better structure my code to
get the information I am after?

Alex.