[Bioperl-l] LocusLink Parsing Problem

[Paul Boutros]

Hello,

I'm trying to work with the SeqIO locuslink parser, and I think I've found
a problem, but I'm not entirely sure.  The problem is that certain values
do not seem to be parsed into the AnnotationCollection.  For example, if
I try to extract all the UniGene clusters:

my $seqio = Bio::SeqIO->new(
			-format	=> 'locuslink',
			-file	=> $file
			);

my $x = 0;

while (my $seq = $seqio->next_seq()) {
	my $ann = $seq->annotation();
	my @uni = $ann->get_Annotations('UNIGENE');
	if (scalar(@uni)) { $x++ }
	}

print "$x\n";

The return is 0.  And that's supported if I check the AnnotationCollection
to see if the key 'UNIGENE' exists in $ann->get_all_annotation_keys() it
never is.  I guess the data must be going somewhere else, but I can't find
it!

I'm using a copy from CVS on February 1st, along with WinXP SP1 and PERL
5.8.0.  

Any ideas where the cluster numbers are going?
Paul