/ 
bioperl-1.5.2_004-RCf
/ Bio::SeqIO::entrezgene

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.

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

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:

http://bugzilla.open-bio.org/

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