[Bioperl-l] LocusLink IO

[Hilmar Lapp]

The input file needs to be the LL_tmpl or in that format. Does your 
input file satisfy this? (NCBI releases several files for LL. Many 
are in tab-format; the LL_tmpl format is a tagged-line format.)

	-hilmar

On Thursday, November 28, 2002, at 03:05 PM, Paul Boutros wrote:

> 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
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
>
--
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------