Provided by: libbio-perl-perl_1.7.2-3_all bug

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

   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/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       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.

   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/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