Provided by: libbio-asn1-entrezgene-perl_1.730-1_all bug


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


       version 1.73


          use Bio::SeqIO;

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


       This is EntrezGene ASN bioperl parser. It is built on top of Bio::ASN1::EntrezGene, a low
       level ASN parser built by Mingyi Liu (<>). 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";


       To do:


       To do: process GO


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       Stefan Kirov <>


       This software is copyright (c) by Stefan Kirov <>.

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