[Bioperl-l] Phylip error

[Jonathan Manning]

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
> >
> > _______________________________________________
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> > Bioperl-l at portal.open-bio.org
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> >
> 
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
>