[Bioperl-l] Error when parsing MEME file

[Amonida Zadissa]

Thanks for the help, it works fine now!

Thanks for your suggestion about the accession numbers, true I do
have a wide range of them in my files but the ID length hasn't
been a problem yet. But I do have parsers if I need to make them
shorter.

Cheers,
Amonida

On Thu, May 06, 2004 at 08:29:04AM -0400, Jason Stajich wrote:
> Something was still wrong with your fix stefan - I committed
> something which should work.  Do a CVS update Amonida and you
> should have thefix.
>
> As for whether or not Seqio can parse long IDs, it just takes
> whatever is after the > until the 1st space.  We don't try and
> interpret the ID and get accession out of the ncbi id lines by
> default - although there have been proposals on the list for
> doing this, I can't really remember if anyone solved it.  I
> just end up writing my own id parser if I need a particular
> thing out...  We solve it for the HitI object when parsing
> blast reports and setting accessions.
>
> -jason
>
> On Thu, 6 May 2004, skirov wrote:
>
> > Amonida, Wow, you have an amazing amount of ids... I am sure
> > it will be much better if you can use a simple ID line like
> >
> > >X61109
> >
> > someseq...  Of course I could change the parser... but I am
> > not sure it is worth it.  Jason, forgive my ignorance, but
> > current SeqIO will not parse fasta ID line like this one:
> >
> > >ref|NW_047562.1|Rn1_2084
> >
> > I guess it will be best if meme parser is in sync with SeqIO
> > with respect to IDs.  Stefan
> >
> > >===== Original Message From Amonida Zadissa
> > ><amonida at sanger.otago.ac.nz>
> >
> > =====
> >
> > >Stefan and Jason,
> > >
> > >Thanks for your replies. I was using bioperl-1.4 but now I
> > >have bioperl-live installed. Nevertheless, the problem seems
> > >to be there but I get new warnings complainging about both
> > >strands now.
> > >
> > >Argument "-" isn't numeric in addition (+) at
> > >/opt/share/perl/5.8.3/Bio/LocatableSeq.pm line 167, <GEN0>
> > >line 699.  Argument "+" isn't numeric in addition (+) at
> > >/opt/share/perl/5.8.3/Bio/Matrix/PSM/InstanceSite.pm line
> > >106, <GEN0> line 700.
> > >
> > >Could this depend on my installation (which by the way went
> > >fine)?
> > >
> > >I'm attaching the MEME test file I have used.
> > >
> > >Thanks for any help, Amonida
> > >
> > >On Wed, May 05, 2004 at 02:51:12PM -0400, Stefan Kirov
> > >wrote:
> > >
> > >> Fixed now, check it from bioperl-live Stefan
> > >>
> > >> Amonida Zadissa wrote:
> > >>
> > >> >Hi everyone,
> > >> >
> > >> >I'm trying to parse a MEME file using the
> > >> >Bio::Matrix::PSM modules but I'm experiencing problems
> > >> >and was hoping someone on the list could help me.
> > >> >
> > >> >The script is attached below. I get a warning saying the
> > >> >following for each "problematic" instance:
> > >> >
> > >> >Argument "-" isn't numeric in addition (+) at
> > >> >/opt/share/perl/5.8.3/Bio/Matrix/PSM/InstanceSite.pm line
> > >> >106, <GEN0> line 1164.
> > >> >
> > >> >Whenever the strand sign is negative the start position
> > >> >is assigned the sign and the score is assigned the start
> > >> >position, so everything seems to shift one column. This
> > >> >happens only if the strand is negative. Note that
> > >> >'$instance' becomes a Bio::Matrix::PSM::InstanceSite
> > >> >object.
> > >> >
> > >> >Is this a parsing error in "InstanceSite.pm" or is my
> > >> >script somehow wrong?
> > >> >
> > >> >Would appreciate any help and by the way thanks for
> > >> >providing this forum!
> > >> >
> > >> >Cheers, Amonida
> > >> >
> > >> >*********************************************************
> > >> >#!/usr/bin/perl -w
> > >> >
> > >> >use strict use warnings use Bio::Matrix::PSM::IO        ;
> > >> >
> > >> >my $psmIO = new Bio::Matrix::PSM::IO( -file =>
> > >> >'meme.file', -format => 'meme');
> > >> >
> > >> >while (my $psm = $psmIO -> next_psm) { my $instances =
> > >> >$psm -> instances; foreach my $instance (@{ $instances })
> > >> >{ my $start = $instance -> start; my $score = $instance
> > >> >-> score; } }
> > >> >
> > >> >*********************************************************

-- 
Amonida Zadissa
Biochemistry Department
Otago University
Dunedin, New Zealand