Re: [Treesoft-treefam] How to extract 2 or more leaves with the same GID ?
Brought to you by:
lh3lh3
From: Sebastien M. <Seb...@un...> - 2008-08-25 12:57:14
|
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 |