[Biopython] ClastalW and creating own log odd table

[Iddo Friedberg]

For installation instrucitons go here:

http://www.clustal.org/

This varies with your operating system.

On Mon, Jun 20, 2011 at 5:14 PM, George Devaniranjan <devaniranjan at gmail.com
> wrote:

> 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
>>
>
>


-- 
Iddo Friedberg
http://iddo-friedberg.net/contact.html