[Bioperl-l] LocusLink IO

[Paul Boutros]

Yup, I took the release that did have that format.  I will download the
file again tomorrow to verify that it wasn't a bad download issue, but I
had a good checksum on the compressed file.

Visually, it was in the correct format and definitely wasn't
tab-delimited.

Paul

On Thu, 28 Nov 2002, Hilmar Lapp wrote:

> 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
> >
> > _______________________________________________
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> > 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
> -------------------------------------------------------------
>