[Bioperl-l] neighbor.pm

[Elizabeth Williams]

I am pulling down the set of sequences using    eval {$seq 
=$gb->get_Seq_by_id($id);}
from a list of gi identifiers.
The list which stopped Neighbor.pm was:
2522394
10727920
13124364
633631
10579820
25317156
15887696
17934261
17988084
15964148
13474446
15892324
15604167
16124268
19914310
23051232
20906191
37520602
35211596
33862201
33634419
33238784
39933589
27376035
17132771
23041817
1652903
23129777
22295967
33632137
7287834
33862352
22406149
14324888

could this be a problem for my script and if so how is the best way of 
catching the error.

At 13:10 24/02/2004, you wrote:
>can you track it down to a specific dataset which causes the problem?  I
>would first guess that neighbor is failing and we're not detecting that
>very well.  you're getting an empty matrix so that is why names is
>failing.
>
>-jason
>
>On Tue, 24 Feb 2004, Elizabeth Williams wrote:
>
> > Hello,
> > I have a problem running the bit of code below.  I get this message:
> >
> > "Can't call method "names" on an undefined value at
> > 
> /biol/programs/perl580/lib/site_perl/5.8.0/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm
> > line 470."
> >
> > but not all the time - it mostly works but on some alignments it comes up
> > with this error.
> > Any ideas of what the problem is or how to fix it?
> >
> >
> >                          #align sequences
> >                          my @params_align = ('ktuple' => 2, 'matrix' =>
> > 'BLOSUM', 'QUIET' => 1);
> >                          my $factory =
> > Bio::Tools::Run::Alignment::Clustalw->new(@params_align);
> >                          my $seq_array_ref = \@seq_array; # where
> > @seq_array is an array of Bio::Seq objects
> >                          my $aln = $factory->align($seq_array_ref);
> >                          my @params_protdist = ('MODEL' => 'PAM', 'QUIET'
> > => 1);
> >
> >                          my $protdist_factory =
> > Bio::Tools::Run::Phylo::Phylip::ProtDist->new(@params_protdist);
> >
> >                          $protdist_factory->version('3.6');
> >
> >                          my $matrix = $protdist_factory->run($aln);
> >
> >                          my @params_neighbor = ('type'=>'NJ', 'QUIET' 
> => 1);
> >
> >                          my $neighborfactory =
> > Bio::Tools::Run::Phylo::Phylip::Neighbor->new(@params_neighbor);
> >
> >                          $neighborfactory->version('3.6');
> >
> >                          my (@trees) = $neighborfactory->run($matrix);
> >
> >                          my $outtree = new Bio::TreeIO(-file =>
> > ">>geneorigin_results2.xls");
> >
> >                          foreach my $tree (@trees) {
> >
> >                                  $outtree->write_tree($tree);
> >
> >                          }
> >
> > Elizabeth J.B. Williams
> > CNAP
> > Department of Biology
> > University of York
> > York
> > YO10 5YW
> > mobile: 07813149274
> > work: 01904 328757
> > Fax: 01904 328762
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
>
>--
>Jason Stajich
>Duke University
>jason at cgt.mc.duke.edu

Elizabeth J.B. Williams
CNAP
Department of Biology
University of York
York
YO10 5YW
mobile: 07813149274
work: 01904 328757
Fax: 01904 328762