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

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

Here is a list of duplicated entries I found.
All of them seem to come from Schistosoma mansoni species.

Smp_150040.1
Smp_062300
Smp_028100.1
Smp_059750
Smp_136850.1
Smp_165350.1
Smp_138920.1
Smp_176260.1
Smp_159900.1
Smp_074070.1
Smp_061920.1
Smp_093750.1
Smp_103460.1
Smp_060940
Smp_176230.1
Smp_041430.1
Smp_034840.1
Smp_034840.1
Smp_153760.1
Smp_055760
Smp_094050.1
Smp_009650.1
Smp_069130.1
Smp_106130.1
Smp_049300.1
Smp_049300.1
Smp_049300.1
Smp_144010.1
Smp_162800.1
Smp_059290.1
Smp_176200.1
Smp_163420.1
Smp_020920.1
Smp_035200.1
Smp_035200.1
Smp_035200.1
Smp_049600.1
Smp_049600.1
Smp_049600.1
Smp_005070.1
Smp_138680.1
Smp_158110.1
Smp_004470.1
Smp_004470.1
Smp_035720
Smp_147250.1
Smp_128200.1
Smp_149200.1
Smp_149200.1
Smp_076030.1
Smp_033050.1
Smp_033050.1
Smp_004780.1
Smp_158320.1
Smp_064040
Smp_161970.1
Smp_104680.1
Smp_034980.1
Smp_035430.1
Smp_025570.1
Smp_025570.1
Smp_042590.1
Smp_063120.1
Smp_063120.1
Smp_160770.1
Smp_160770.1
Smp_045430.1
Smp_054790.1
Smp_054340.1
Smp_054340.1
Smp_042270.1
Smp_042270.1
Smp_038080.1
Smp_005080.1
Smp_005080.1
Smp_066630.1
Smp_046880.1
Smp_053510.1
Smp_173180.1
Smp_141630.1
Smp_141630.1
Smp_141630.1
Smp_124820.1
Smp_046090.1
Smp_096450
Smp_120320
Smp_075220.1
Smp_075220.1
Smp_000030.1
Smp_000030.1
Smp_076630.1
Smp_030930.1
Smp_142010.1
Smp_038870.1
Smp_050360
Smp_033670.1
Smp_033670.1
Smp_033670.1
Smp_058150.1
Smp_031040
Smp_024060.1
Smp_001410
Smp_031950.1
Smp_009420
Smp_103930.1
Smp_103930.1
Smp_103930.1
Smp_103930.1
Smp_035270.1
Smp_048260.1
Smp_130790.1
Smp_042670.1
Smp_031000.1
Smp_138970.1
Smp_042430.1
Smp_064020.2
Smp_064020.2
Smp_064020.2
Smp_079050.1
Smp_069220
Smp_055420.1
Smp_007630.1
Smp_063580.1
Smp_063580.1
Smp_156440.2
Smp_096780.1
Smp_106080.1
Smp_066960.1
Smp_082560.1
Smp_175120.1
Smp_085310.1
Smp_045750
Smp_140450.1
Smp_010230
Smp_061310.1
Smp_061310.1
Smp_084140.1
Smp_084140.1
Smp_095910.1
Smp_017290.3
Smp_165810.2
Smp_024360
Smp_030920.1
Smp_032580.1
Smp_032580.1
Smp_121430.1
Smp_074500
Smp_000740.1
Smp_066340
Smp_048280.1
Smp_098890.1
Smp_098890.1
Smp_045950.1
Smp_079430.1
Smp_052280.1
Smp_065190
Smp_165140.1
Smp_150850.1
Smp_121610.1
Smp_121610.1
Smp_128890.1
Smp_014400.1
Smp_014400.1
Smp_014400.1
Smp_049730
Smp_168850.1
Smp_101370
Smp_006250.1
Smp_053220.1

Cheers
Sébastien


> 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