[Biopython] ClastalW and creating own log odd table

[Iddo Friedberg]

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