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

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

> 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