[Bioperl-l] Phylip error

[Jonathan Manning]

Many apologies Jason, the problem was down to a faulty symbolic link in
my /usr/bin <hangs head in shame>. Sorry for wasting your time- I'm
getting somewhere with it now. 

That testing thing's useful to know though.....

Thanks again,

Jon

On Wed, 2004-06-02 at 16:28, Jason Stajich wrote:
> 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
>