/ 
FAST-1.06
River stage zero No dependents
/ FAST::Bio::SeqIO::entrezgene

NAME

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

SYNOPSIS

use FAST::Bio::SeqIO;

# don't instantiate directly - instead do
my $seqio = FAST::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 FAST::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 FAST::Bio::AnnotationI objects.

If you need all the data do:

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

The second variable returned, $genestructure, is a FAST::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 = FAST::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 FAST::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://redmine.open-bio.org/projects/bioperl/

AUTHOR - Stefan Kirov

Email skirov at utk.edu

CONTRIBUTORS

Hilmar Lapp, hlapp at gmx.net

APPENDIX

This parser is based on FAST::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