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

[Chris Fields]

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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