[Bioperl-l] Bio::Tools::Run::Phylo::Phyml, tree_string

[Tristan Lefebure]

Ouups, I found a typo in my post, it should read:

I am not quite sure I understand why tree_string() from
Bio::Tools::Run::Phylo::Phyml returns
a string that looks like that (I removed the end of the tree):

BIONJ(((((((('92':0.0114354726,'12':0.0472591023)0.0000000000:0.0000005859,...

On Tue, Jul 26, 2011 at 4:47 PM, Tristan Lefebure
<tristan.lefebure at gmail.com> wrote:
> Hi there,
> I am not quite sure I understand why tree_string() from Bio::Tools::Run::Phylo::Phyml returns
> a string that looks like that (I removed the end of the tree):
>
> Tree is BIONJ(((((((('92':0.0114354726,'12':0.0472591023)0.0000000000:0.0000005859,...
>
> Why do we have this 'Tree is BIONJ' thing?
>
> A quick look at the code in the _run() function gives :
>
>        {
>        open(my $FH_TREE, "<", $tree_file)
>            || $self->throw("Phyml call ($command) did not give an output: $?");
>        local $/;
>        $self->{_tree} .= <$FH_TREE>;
>    }
>
> Why appending something to $self->{_tree}? What about?
>        $self->{_tree} = <$FH_TREE>;
>
> I was about to fill a bug report, but then I saw that in Phyml.t:
>
>    is substr($factory->tree_string, 0, 9), 'BIONJ(SIN', 'tree_string()';
>
> Well, I am lost. Any help much appreciated...
>
> --
> Tristan
>