NAME

Bio::SeqIO::entrezgene - Entrez Gene ASN1 parser

SYNOPSIS

   use Bio::SeqIO;
   # don't instantiate directly - instead do
   my $seqio = Bio::SeqIO->new(-format => 'entrezgene',
                               -file => $file);
   my $gene = $seqio->next_seq;

DESCRIPTION

This is EntrezGene ASN bioperl parser. It is built on top of Bio::ASN1::EntrezGene, a low level ASN parser built by Mingyi Liu (<http://sourceforge.net/projects/egparser>). The easiest way to use it is shown above.

You will get most of the Entrez Gene annotation such as gene symbol, gene name and description, accession numbers associated with the gene, etc. Almost all of these are given as Bio::AnnotationI objects.

If you need all the data do:

   my $seqio = Bio::SeqIO->new(-format => 'entrezgene',
                               -file => $file,
                               -debug => 'on' );
   my ($gene,$genestructure,$uncaptured) = $seqio->next_seq;

The second variable returned, $genestructure, is a Bio::Cluster::SequenceFamily object. It contains all Refseqs and the genomic contigs that are associated with the particular gene. The third variable, $uncaptured, is a reference to a plain array.

You can also modify the output to allow back compatibility with the old LocusLink parser:

   my $seqio = Bio::SeqIO->new(-format => 'entrezgene',
                               -file => $file,
                               -locuslink => 'convert');

The "-debug" and "-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";
    }
  }

FEEDBACK

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Stefan Kirov

Email skirov at utk.edu

CONTRIBUTORS

Hilmar Lapp, hlapp at gmx.net

APPENDIX

This parser is based on Bio::ASN1::EntrezGene module.

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

_process_products_coordinates

To do:

_process_prop

To do: process GO