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Bio-ASN1-EntrezGene-1.73
River stage two • 2 direct dependents • 11 total dependents
/ Bio::SeqIO::entrezgene

NAME

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

VERSION

version 1.73

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";
  }
}

_process_products_coordinates

To do:

_process_prop

To do: process GO

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/Support.html    - 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/bio-asn1-entrezgene/issues

AUTHOR

Stefan Kirov <skirov@utk.edu>

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.