[Bioperl-l] Bugz in Consense

[Brian Osborne]

Devin,

>apologies if there is a better way of submitting fixes than mailing the

The best way is still http://bugzilla.bioperl.org/ since once it's entered
there it will never be forgotten.

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Devin Scannell
Sent: Thursday, September 16, 2004 6:53 AM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] Bugz in Consense

Hi,

was having some trouble setting the outgroup when drawing trees with
phylip and tracked the problem down to here (changes marked with ###) :

Consense.pm

sub _set_names_from_tree {
   my ($self,$tree) = @_;
   my $newick;
   my $ios = IO::String->new($newick);
   my $tio = Bio::TreeIO->new(-fh=>$ios,-format=>'newick');
   $tio->write_tree($tree);

### changed \w to [\w\._]
### newick allows at least these and I think a few other symbols

   my @names = $newick=~/([\w\._]+):\d+/g;
   my %names;

### changed < to <=

   for(my $i=0; $i <= $#names; $i++){
       $names{$names[$i]} = $i+1;
   }
   $self->names(\%names);

   return;
}

apologies if there is a better way of submitting fixes than mailing the
the whole list... but better to err on the side of caution, right?

regards,

Devin

_______________________________________________
Bioperl-l mailing list
Bioperl-l at portal.open-bio.org
http://portal.open-bio.org/mailman/listinfo/bioperl-l