[ensembl-dev] Affymetrix Probesets

[Nathan Johnson]

Hi Alex

This code looks like is is trying to get the probe/set xref info from the core DB. These data were moved to the funcgen DB quite some time ago.

For some example on how to retrieve PorbeSet level annotation see this doc:

	http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl-functgenomics/scripts/examples/microarray_annotation_example.pl?revision=1.3&root=ensembl&view=markup

Thanks

Nath

On 14 Jun 2011, at 15:32, Alex Kalderimis wrote:

> 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.
> 
> 
> 
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Nathan Johnson
Senior Scientific Programmer
Ensembl Regulation
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD

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