[Bioperl-l] Parsing Entrez Gene ASN.1

Stefan Kirov stefan.kirov at bms.com
Wed Nov 28 17:16:18 EST 2007


Here is an example for GO, will send the one for KEGG later:
my $eio=new Bio::SeqIO(-file=>$file,-format=>'entrezgene',
 	-service_record=>'yes');#, -locuslink=>'convert');
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'); #Do not need STS markers
     		my $evid=$ot->comment;
     		$evid=~s/evidence: //i;
     		my @ref=$ot->term->get_references; #Really there should be just one?
     		my $id=$ot->identifier;
     		my $fid='GO:' . sprintf("%07u",$id);
     		print join("\t",$gid,$ot->ontology->name,$ot->name,$evid,$fid, at ref?$ref[0]->medline:''),"\n";
 	}
}
Please note there is a bug in the parser that makes it suck a lot of RAM. 
I am fixing this and will commit probably by the week's end- you will have 
to update at that point. If you work with few records this should not 
matter.
Stefan


On Thu, 29 Nov 2007, Smithies, Russell wrote:

> Has anyone got a good example of parsing ASN.1 with
> Bio::SeqIO::entrezgene?
> I'm trying to get GO ids and KEGG terms out but it's quite deeply nested
> and my Perl isn't that good  :-(
>
> Russell
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