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

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

It works properly for families I tested.
Thanks

Best regards
Sébastien

> Hi,
> 
> I have fixed the API. You'll need to check out the new Tree.pm module 
> from the
> Subversion repository. As I am on holidays I have only just quickly 
> tested the
> changes. Let me know if it doesn't work.
> 
> Cheers
> 
> J-K
> 
> Quoting Sebastien MORETTI <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
>> S=E9bastien
>>
>>
>>> 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
>>> S=E9bastien
>>> =
>>
>>>>> 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 th=
>> e =
>>
>>>>> 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
>>>> S=E9bastien
>>>>
>>>>> 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 =
>> =3D
>>>>>>
>>>>>> 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 & =
>> =3D
>>>>>>
>>>>>> Smp_150040.2
>>>>>> But the get_alignment method returns twice Smp_150040.1, with the 
>>>>>> same=
>> =3D
>>>>>>
>>>>>> 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