[Biopython] ClastalW and creating own log odd table

[George Devaniranjan]

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