treesoft-treefam

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

[Sebastien M. <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

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

Re: [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

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

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