[Bioperl-l] LocusLink IO

[Paul Boutros]

Hi all,

I'm using the LocusLink SeqIO parser with a download of LocusLink from
NCBI today (LL3_021128.txt).  When I just parse through the file doing
nothing except for checking the organism annotation with:

use Bio::SeqIO;

my $seqio = Bio::SeqIO->new(
			-format	=> 'locuslink',
			-file	=> 'LL3_021128.txt'
			);

while (my $acc = $seqio->next_seq()->annotation()) {
	if ($acc->get_Annotations('ORGANISM') =~ /rattus norvegicus/i) {
		print "Rat!\n";
		}
	}

I get:

Deep recursion on subroutine "Bio::SeqIO::locuslink::next_seq" at
C:/Perl/site/lib/Bio\SeqIO\locuslink.pm line 456, <GEN0> chunk 15465.
Deep recursion on subroutine "Bio::SeqIO::locuslink::next_seq" at
C:/Perl/site/lib/Bio\SeqIO\locuslink.pm line 456, <GEN0> chunk 15595.


------------- EXCEPTION  -------------
MSG: No LOCUSID in first line of record. Not LocusLink in my book.
STACK Bio::SeqIO::locuslink::next_seq 
C:/Perl/site/lib/Bio\SeqIO\locuslink.pm:435
STACK toplevel testLL.pl:10
--------------------------------------

Interestingly enough I also don't get any output from the ORGANISM check,
so I must be doing that wrong, too.  I notice that the thing processes a
fair chunk of time before spitting out the two "Deep recursion" warnings,
and then a fair bit longer before hitting the exception.

Any ideas if I'm doing something unusual, or if maybe I should submit this
as a bug report?

Paul

OS: Win XP SP 1 and Win2K SP2
Perl: 5.8.0 and 5.6.1
BioPerl: CVS yesterday