[Bioperl-l] LocusLink Parsing Problem

[Hilmar Lapp]

They end up as db_xrefs (Bio::Annotation::DBLink instances under key 
'dblink').

	-hilmar

On Tuesday, February 11, 2003, at 02:45  PM, Paul Boutros wrote:

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