[Bioperl-l] LocusLink IO
Paul Boutros
pcboutro@engmail.uwaterloo.ca
Fri, 29 Nov 2002 17:52:40 -0500 (EST)
Hi again,
I don't encounter any problems parsing the test file:
t\data\LL-sample.seq
If I run the LocusLink test
c:\perl\bioperl-live> perl -w t\LocusLink.t
1..23
ok 1
ok 2
Use of uninitialized value in pattern match (m//) at
C:/Perl/site/lib/Bio\SeqIO\embl.pm line 384, <GEN0> line 2.
Use of uninitialized value in transliteration (tr///) at
C:/Perl/site/lib/Bio\SeqIO\embl.pm line 600, <GEN0> line 2.
Use of uninitialized value in transliteration (tr///) at
C:/Perl/site/lib/Bio\SeqIO\embl.pm line 603, <GEN0> line 2.
Use of uninitialized value in transliteration (tr///) at
C:/Perl/site/lib/Bio\SeqIO\embl.pm line 604, <GEN0> line 2.
Use of uninitialized value in transliteration (tr///) at
C:/Perl/site/lib/Bio\SeqIO\embl.pm line 605, <GEN0> line 2.
Use of uninitialized value in transliteration (tr///) at
C:/Perl/site/lib/Bio\SeqIO\embl.pm line 606, <GEN0> line 2.
Use of uninitialized value in length at C:/Perl/site/lib/Bio\SeqIO\embl.pm
line 618, <GEN0> line 2.
Use of uninitialized value in substr at C:/Perl/site/lib/Bio\SeqIO\embl.pm
line 633, <GEN0> line 2.
Use of uninitialized value in pattern match (m//) at
C:/Perl/site/lib/Bio\SeqIO\embl.pm line 384, <GEN0> line 3.
Use of uninitialized value in transliteration (tr///) at
C:/Perl/site/lib/Bio\SeqIO\embl.pm line 600, <GEN0> line 3.
Use of uninitialized value in transliteration (tr///) at
C:/Perl/site/lib/Bio\SeqIO\embl.pm line 603, <GEN0> line 3.
Use of uninitialized value in transliteration (tr///) at
C:/Perl/site/lib/Bio\SeqIO\embl.pm line 604, <GEN0> line 3.
Use of uninitialized value in transliteration (tr///) at
C:/Perl/site/lib/Bio\SeqIO\embl.pm line 605, <GEN0> line 3.
Use of uninitialized value in transliteration (tr///) at
C:/Perl/site/lib/Bio\SeqIO\embl.pm line 606, <GEN0> line 3.
Use of uninitialized value in length at C:/Perl/site/lib/Bio\SeqIO\embl.pm
line 618, <GEN0> line 3.
Use of uninitialized value in substr at C:/Perl/site/lib/Bio\SeqIO\embl.pm
line 633, <GEN0> line 3.
ok 3
and okay through the rest of the tests.
Visually the two files look very similar, and there are no obvious
formatting differences. And it does take quite a few seconds of running
before the two "Deep Recursion" warnings come up, then a few more before I
get the exception.
When I run:
use Bio::SeqIO;
use strict;
my $file = $ARGV[0];
my $seqio = Bio::SeqIO->new(
-format => 'locuslink',
-file => $file
);
while (my $seq = $seqio->next_seq()) {
my $acc = $seq->annotation();
print $seq->accession(), "\n";
}
The two deep recursion warnings come as:
15601
Deep recursion on subroutine "Bio::SeqIO::locuslink::next_seq" at
C:/Perl/site/lib/Bio\SeqIO\locuslink.pm line 456, <GEN0> chunk 15465.
15731
Deep recursion on subroutine "Bio::SeqIO::locuslink::next_seq" at
C:/Perl/site/lib/Bio\SeqIO\locuslink.pm line 456, <GEN0> chunk 15595.
15874
15890
And the exception is thrown as:
24785
24786
24787
------------- 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:11
--------------------------------------
On Fri, 29 Nov 2002, Hilmar Lapp wrote:
> 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
> > > -------------------------------------------------------------
> > >
> >
> >
>