[Biopython] ClastalW and creating own log odd table

[George Devaniranjan]

Thank you Iddo,
Could I also ask if I should install ClustalW within the
python2.4/site-packages
or somewhere else?
Thank you for your answers,
George


On Mon, Jun 20, 2011 at 5:05 PM, Iddo Friedberg <idoerg at gmail.com> wrote:

> Clustalw is a 3rd party package, it is not part of Biopython.
>
> What you are importing via Python is not clustalw, but rather the Biopython
> interface to clustalw.
>
> ./I
>
>
> On Mon, Jun 20, 2011 at 4:49 PM, George Devaniranjan <
> devaniranjan at gmail.com> wrote:
>
>> Hi Iddo,
>>
>> Thank you but when I do
>>
>> from Bio import Clustalw
>>
>> It does not raise an error, and under
>> Python2.4/Site-Packages/Bio/
>> There is a folder called ClustalW
>>
>> So does it mean there is something extra to be installed than the above
>> which already exist?
>>
>> Thank you,
>> George
>>
>>
>>
>> On Mon, Jun 20, 2011 at 4:43 PM, Iddo Friedberg <idoerg at gmail.com> wrote:
>>
>>> George,
>>>
>>> It seems like wither you do no have clustalw installed, or it is not
>>> installed in your normal path. Clustalw is a 3rd party program,
>>> unaffiliated with biopython. To download and install, go here:
>>> http://www.clustal.org/
>>>
>>> Iddo
>>>
>>>
>>>
>>> On Mon, Jun 20, 2011 at 4:35 PM, George Devaniranjan <
>>> devaniranjan at gmail.com> wrote:
>>>
>>>> I want to try set up a log-odds matrix for my own and was experimenting
>>>> with
>>>> the BIOPYTHON TUTURIOL
>>>>
>>>>
>>>> import os
>>>> from Bio import Clustalw
>>>> from Bio.Clustalw import MultipleAlignCL
>>>> cline=MultipleAlignCL(os.path.join(os.curdir, 'sequence.fasta')
>>>> cline.set_output('test.aln')
>>>>
>>>> alignment =Clustalw.do_alignment(cline)
>>>>
>>>>
>>>> The output was as follows..........
>>>>
>>>> sh: clustalw: command not found
>>>> Traceback (most recent call last):
>>>>  File "<stdin>", line 1, in ?
>>>>  File "/usr/local/lib/python2.4/site-packages/Bio/Clustalw/__init__.py",
>>>> line 134, in do_alignment
>>>>    raise IOError("Output .aln file %s not produced, commandline: %s"
>>>> IOError: Output .aln file test.aln not produced, commandline: clustalw
>>>> ./sequence.fasta -OUTFILE=test.aln
>>>>
>>>>
>>>> I am not sure where I am going wrong.
>>>> Thank you,
>>>> George
>>>> _______________________________________________
>>>> Biopython mailing list  -  Biopython at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/biopython
>>>>
>>>
>>>
>>>
>>> --
>>> Iddo Friedberg
>>> http://iddo-friedberg.net/contact.html
>>>
>>
>>
>
>
> --
> Iddo Friedberg
> http://iddo-friedberg.net/contact.html
>