[Bioperl-l] LocusLink IO

[Hilmar Lapp]

I will check what's happening. There is a test case and a sample file in the repository; while you're at it, do you see what the fundamental difference is between the sample and the your input file? (Or does the test fail as well for you?)

	-hilmar

> -----Original Message-----
> From: Paul Boutros [mailto:pcboutro@engmail.uwaterloo.ca]
> Sent: Friday, November 29, 2002 9:21 AM
> To: Hilmar Lapp
> Cc: bioperl-l@bioperl.org
> Subject: Re: [Bioperl-l] LocusLink IO
> 
> 
> I tried again on today's (11/29/2002) LL_tmpl file and same error:
> 
> C:\paul\dev\LocusLink>perl -w testLL.pl
> 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:8
> 
> --------------------------------------
> 
> 
> 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
> > >
> > > _______________________________________________
> > > 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
> > -------------------------------------------------------------
> > 
> 
>