[Bioperl-l] neighbor.pm

[Jason Stajich]

There is a 'bad' amino acid in your data.

I get this when I run phylip protdist by hand on your data:
 WARNING -- BAD AMINO ACID:U AT POSITION 1206 OF SPECIES  32
offending base is a 'U'
[jason at sonogno jason]$ seqret -sbegin 1205 -send 1207 out.aln.fasta:AAF44872/1-3 stdout
Reads and writes (returns) sequences
>AAF44872/1-3
-U-

So you'll need to prune these out of the data I guess.

-jason

On Tue, 24 Feb 2004, Elizabeth Williams wrote:

> Here is the alignment.
>
> At 14:06 24/02/2004, you wrote:
> >Any chance you can save the multiple sequence alignment and send that out
> >instead?
> >-jason
> >
> >On Tue, 24 Feb 2004, Elizabeth Williams wrote:
> >
> > > 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
> > >
> >
> >--
> >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
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu