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

[Jason Stajich]

Heikki - 
can you take a look at this when you get time - I'm unclear what the BIONJ string is used for?


Begin forwarded message:

> From: Tristan Lefebure <tristan.lefebure at gmail.com>
> Date: July 27, 2011 6:12:16 AM AKDT
> To: bioperl mailing list <bioperl-l at lists.open-bio.org>
> Subject: Re: [Bioperl-l] Bio::Tools::Run::Phylo::Phyml, tree_string
> 
> done:
> https://redmine.open-bio.org/issues/3273
> 
> --
> Tristan
> 
> On Tue, Jul 26, 2011 at 9:43 PM, Chris Fields <cjfields at illinois.edu> wrote:
>> That's an odd one.  Could you file this on redmine?
>> 
>> chris
>> 
>> On Jul 26, 2011, at 10:14 AM, Tristan Lefebure wrote:
>> 
>>> 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
>>>> 
>>> 
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>> 
>> 
> 
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