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examples/parse_entrez_gene_example.pl  view on Meta::CPAN

    }
  }
  if($genestart && $geneend)
  {
    # user can decide how to store
  }

  # tracking info about how this gene has changed
  if(safeval($seq, '{track-info}->[0]->{current-id}'))
  {
    my (@ids, $newegid, $newllid);
    foreach my $id (@{$seq->{'track-info'}->[0]->{'current-id'}})
    {
      my $tmpid = safeval($id, '{tag}->[0]->{id}');
      push(@ids, "$id->{db}:$tmpid");
      $newegid = $tmpid if($id->{db} =~ /^GeneID$/i);
      $newllid = $tmpid if($id->{db} =~ /^LocusID$/i);
    }
    my $comment = "Gene moved: current IDs are: " . join(' ; ', @ids);
  }

  return $llgene;
}

# safely assign a value to $data->{$key} ($data must be hash)
sub safeassign

lib/Bio/SeqIO/entrezgene.pm  view on Meta::CPAN

The C<-debug> and C<-locuslink> options slow down the parser.

Example code which looks for ontology terms:

  my $eio = new Bio::SeqIO(-file => $file,
                           -format => 'entrezgene',
                           -service_record => 'yes');

  while (my $seq = $eio->next_seq) {
    my $gid = $seq->accession_number;
    foreach my $ot ($ann->get_Annotations('OntologyTerm')) {
      next if ($ot->term->authority eq 'STS marker'); # No STS markers
      my $evid = $ot->comment;
      $evid =~ s/evidence: //i;
      my @ref = $ot->term->get_references;
      my $id = $ot->identifier;
      my $fid = 'GO:' . sprintf("%07u",$id);
      print join("\t",$gid, $ot->ontology->name, $ot->name, $evid,
        $fid, @ref?$ref[0]->medline:''), "\n";
    }
  }

=head1 _process_products_coordinates

To do:

=head1 _process_prop