[Bioperl-l] Phylip error

[Jason Stajich]

what does
% cd bioperl-run
% perl -I. -w t/ProtDist.t

say?

Which version bioperl-run are you using

-jason

On Wed, 2 Jun 2004, Jonathan Manning wrote:
> Thanks for the reply. I'm using version 3.5. Although I may only do a
> simple run right now, I'd like to allow for future extension, so
> integration of the Phylip suite is desirable.
>
> I'm unsure of what you mean about the test, could you clarify?
>
> Thanks,
>
> Jon
>
> On Wed, 2004-06-02 at 15:05, Jason Stajich wrote:
> > Does the protdist test work fine for you in bioperl-run?
> >
> > Are you using phylip 3.5 or 3.6?  You need to twiddle something to use 3.6
> > bash% export PHYLIPVERSION = 3.6
> >
> > or in your script:
> > $ENV{PHYLIPVERSION} = 3.6;
> > use Bio::Tools::Run::Phylo::Phylip::ProtDist;
> >
> > If you are just doing kimura 2P you can avoid ProtDist completely with new
> > code in Bio::Align::ProteinStatistics.
> >
> > -jason
> > On Wed, 2 Jun 2004, Jonathan Manning wrote:
> >
> > > Hi to all,
> > >
> > > I'm trying to incorporate phylogenetic analysis into a script I'm
> > > writing. I'm attempting to feed in alignments (SimpleAlign objects)
> > > derived from an earlier subroutine, and stored in a global hash (the
> > > reason for the hash being that I wanted to reference by a blast query
> > > sequence). My code:
> > >
> > > sub phylip{
> > >
> > > 	foreach my $key (keys %alignments){
> > > 		my ($alnmnt) = $alignments{$key};
> > > 		my @params = ('MODEL' => 'PAM');
> > > 		my $protdist = Bio::Tools::Run::Phylo::Phylip::ProtDist->new(@params);
> > >   		my $matrix  = $protdist->run($alnmnt);
> > > 		@params = ('type'=>'NJ','outgroup'=>2,'lowtri'=>1,
> > >              'upptri'=>1,'subrep'=>1);
> > >
> > >   		my $neighbor =
> > > Bio::Tools::Run::Phylo::Phylip::Neighbor->new(@params);
> > > 		my ($tree) = $neighbor_factory->run($matrix);
> > > 	}
> > >
> > > }
> > >
> > >
> > >
> > > It seems to have a problem at the protdist stage, resulting in the
> > > following error:
> > >
> > >
> > >
> > > ------------- EXCEPTION  -------------
> > > MSG: protdist did not create matrix correctly (/tmp/q4lIZVPNvW/outfile)
> > > STACK Bio::Tools::Run::Phylo::Phylip::ProtDist::_run
> > > /usr/lib/perl5/site_perl/5.8.3/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm:407
> > > STACK Bio::Tools::Run::Phylo::Phylip::ProtDist::run
> > > /usr/lib/perl5/site_perl/5.8.3/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm:364
> > > STACK main::phylip ./GeneInfo5.pl:1648
> > > STACK toplevel ./GeneInfo5.pl:563
> > >
> > > --------------------------------------
> > >
> > >
> > > >From the archives, this would seem to be a problem with writing the
> > > matrix to file, but I don't know why. The permissions on /tmp are fine.
> > >
> > > Does anyone have any ideas?
> > >
> > > Thanks in advance,
> > >
> > > Jon
> > >
> > > _______________________________________________
> > > 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
> >
>

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