[Bioperl-l] Locuslink parser

Hilmar Lapp hlapp at gnf.org
Thu Feb 12 14:09:51 EST 2004

On Thursday, February 12, 2004, at 09:46  AM, Law, Annie wrote:

> I am most intereste in obtaining the fields  locuslink id, GO id, 
> accession number, unigene id.

The locuslink ID is the $seq->accession_number. GO should be there as 
term annotations, unigene ID and other accessions should be present as 
dbxref annotations.

You can test for an annotation being a term annotation or a dbxref:

	foreach my $ann (@annotations) {
		if ($ann->isa("Bio::Ontology::TermI")) {
			# this is an ontology term as annotation
		if ($ann->isa("Bio::Annotation::DBLink")) {
			# this is a dbxref annotation

Using the map function you can easily filter for annotation types, for 

	@term_annotations = map { $_->isa("Bio::Ontology::TermI"); } 

BTW if you want to get all annotations from a seq object, you can just 
say $seq->get_Annotations() and omit the key.


Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757

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