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