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=encoding UTF-8

=head1 NAME

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

=head1 VERSION

version 1.73

=head1 SYNOPSIS

   use Bio::SeqIO;

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

=head1 DESCRIPTION

This is EntrezGene ASN bioperl parser. It is built on top of
L<Bio::ASN1::EntrezGene>, a low level ASN parser built by Mingyi Liu
(L<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  L<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, C<$genestructure>, is a L<Bio::Cluster::SequenceFamily>
object. It contains all Refseqs and the genomic contigs that are associated
with the particular gene. The third variable, C<$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 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

To do: process GO

=head1 FEEDBACK

=head2 Mailing lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.

  bioperl-l@bioperl.org              - General discussion
  http://bioperl.org/Support.html    - About the mailing lists

=head2 Support

Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>

rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.

=head2 Reporting bugs

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:

  https://github.com/bioperl/bio-asn1-entrezgene/issues

=head1 AUTHOR

Stefan Kirov <skirov@utk.edu>

=head1 COPYRIGHT

This software is copyright (c) by Stefan Kirov <skirov@utk.edu>.

This software is available under the same terms as the perl 5 programming language system itself.

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