[Biopython] ClastalW and creating own log odd table

[Iddo Friedberg]

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