Re: [Treesoft-devel] [Treesoft-treefam] How to extract 2 or more leaves with the same GID ?

[Sebastien M. <Seb...@un...>]

Maybe the best way will be to remove redundancy into the gene list (from 
leaves) because I get 2 Smp_150040 entries.

Then extract alignment(s) for every geneID.


What do you think about ?

Cheers
Sébastien

>> Hi Sebastien,
>>
>> The example you give looks strange because a gene should only be 
>> represented by
>> one transcript in a given tree.
> 
> I think I can find several other examples like this one.
> 
>> Anyone got an idea why a gene can be represented by 2 transcripts in the 
>> same
>> tree ?
> 
> It seems these transcripts are too distant and that they cannot be 
> merged as one single gene.
> 
>> I'll see how to fix the API for cases like this.
>  >
>> Cheers
>>
>> J-K
> 
> Thanks
> Sébastien
> 
>> Quoting Sebastien MORETTI <Seb...@un...>:
>>
>>> Hi,
>>>
>>> we use your API which is very powerful.
>>> But there is a problem when we try to get the alignment for families =
>>>
>>> where one GID (GeneID) is the same for 2 or more leaves:
>>> e.g.     1 Family     TF101024
>>>     1 GID         Smp_150040
>>>     2 leaves    Smp_150040.1 & Smp_150040.2
>>>
>>> the nhx method returns the proper tree with distinct Smp_150040.1 & =
>>>
>>> Smp_150040.2
>>> But the get_alignment method returns twice Smp_150040.1, with the same =
>>>
>>> headers and sequences. Smp_150040.1 is duplicated.
>>>
>>>
>>> How to resolve this ?
>>>
>>> Thanks

-- 
Sébastien Moretti
Department of Ecology and Evolution,
Biophore, University of Lausanne,
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4221/4056