[Bioperl-l] problem with neighbor.pm

[Jason Stajich]

either set the env variable PHYLIPVERSION in your shell or at the top of your script
$ENV{PHYLIPVERSION} = '3.6';
(before any use ... statements)

Or the less ideal, setting per Phylip factory object your create, i.e.:
 $protdist_factory->version('3.6');
 $neighborfactory->version('3.6');

-jason
On Wed, 4 Feb 2004, Elizabeth Williams wrote:

> i am using 3.6.  Which setting needs to be twiddled?
>
> At 13:23 04/02/2004, you wrote:
> >phylip 3.5 or 3.6? -- you may need to twiddle one setting if you are using
> >phylip 3.6
> >
> >
> >-jason
> >On Wed, 4 Feb 2004, Elizabeth Williams wrote:
> >
> > > Hello,
> > >
> > > I am trying to run the phylip modules on a set of Bio::seq sequences.  I
> > > have run into a problem with neighbor.pm  The module runs the program but
> > > then loses the tree somehow and comes up with this error message.
> > >
> > > ------------- EXCEPTION: Bio::Root::Exception -------------
> > > MSG: neighbor did not create tree correctly (expected
> > /tmp/lHCvy7ByeN/treefile)
> > > STACK: Error::throw
> > > STACK: Bio::Root::Root::throw
> > > /biol/programs/perl580/lib/site_perl/5.8.0/Bio/Root/Root.pm:328
> > > STACK: Bio::Tools::Run::Phylo::Phylip::Neighbor::_run
> > >
> > /biol/programs/perl580/lib/site_perl/5.8.0/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm:412
> > > STACK: Bio::Tools::Run::Phylo::Phylip::Neighbor::run
> > >
> > /biol/programs/perl580/lib/site_perl/5.8.0/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm:353
> > > STACK: Bio::Tools::Run::Phylo::Phylip::Neighbor::create_tree
> > >
> > /biol/programs/perl580/lib/site_perl/5.8.0/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm:370
> > > STACK: geneorigin.pl:74
> > > -----------------------------------------------------------
> > >
> > > The script I am using is below.
> > > Anyone have any ideas what is causing the problem?  I am at a loss.
> > >
> > > use Bio::DB::GenPept;
> > > use Bio::Tools::Run::Alignment::Clustalw;
> > > use Bio::Tools::Run::Phylo::Phylip::ProtDist;
> > > use Bio::Tools::Run::Phylo::Phylip::Neighbor;
> > >
> > > #use strict;
> > > use Bio::SeqIO;
> > > use Bio::Seq;
> > > use Bio::AlignIO;
> > > use Bio::SimpleAlign;
> > >
> > > $ENV{PHYLIPDIR} = '/biol/programs/phylip/exe';
> > > .
> > > .
> > > .
> > > .
> > > .
> > > .
> > >                          my @params_align = ('ktuple' => 2, 'matrix' =>
> > > 'BLOSUM');
> > >                          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 created earlier
> > >                          my $aln = $factory->align($seq_array_ref);
> > >                          my @params_protdist = ('MODEL' => 'PAM');
> > >
> > >                          my $protdist_factory =
> > > Bio::Tools::Run::Phylo::Phylip::ProtDist->new(@params_protdist);
> > >
> > >                          my $matrix = $protdist_factory->run($aln);
> > >
> > >                          my @params_neighbor = ('type'=>'NJ');
> > >
> > >
> > >
> > >                          my $neighborfactory =
> > > Bio::Tools::Run::Phylo::Phylip::Neighbor->new(@params_neighbor);
> > >
> > >                          my $tree = $neighborfactory->create_tree($matrix);
> > >
> > >
> > > Elizabeth J.B. Williams
> > >
> > > _______________________________________________
> > > 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