[BioPython] do_alignment

[Peter]

On Tue, Jan 6, 2009 at 9:58 AM, Seda Alper <sedaalper at yahoo.com> wrote:
>
> Hi Peter,
>
> I applied what you do. However now the error is like that
>
> import os
> from Bio.Clustalw import MultipleAlignCL
>
> clustalw_exe = r"C:\Python\Biopython-1.49\clustalw_exe"

The above is wrong - the filename should end with ".exe", so it might be this:

clustalw_exe = r"C:\Python\Biopython-1.49\clustalw.exe"

(assuming you really do have the ClustalW executable in your Biopython
directory)

> assert os.path.isfile(clustalw_exe)
> cline = MultipleAlignCL(os.path.join(os.curdir,"opuntia.fasta"),clustalw_exe)
> ...
> Traceback (most recent call last):
>  File "C:\Python25\ders\se.py", line 5, in <module>
>    assert os.path.isfile(clustalw_exe)
> AssertionError

The assertion failed becase the Clustalw  filename you used does not exist.

Peter