[BioPython] Clustalw Problems
Peter
biopython at maubp.freeserve.co.uk
Wed Apr 8 21:50:24 UTC 2009
On 4/8/09, Bradley Hintze <bradley.h at aggiemail.usu.edu> wrote:
> Hi,
>
> I am having a hard time running an alignment. I am running in windows and
> here is my code and the error message that I get after running do_alignment.
>
> >>> import os
> >>> from Bio.Clustalw import MultipleAlignCL
> >>> from Bio.Clustalw import do_alignment
> >>> cline=MultipleAlignCL(r"C:\Documents and
> Settings\student\Desktop\Foo\mtr4.fasta", r"C:\Program
> Files\clustalw1.83.XP\clustalw.exe")
> >>> cline.set_output(r"C:\Documents and
> Settings\students\Desktop\Foo\test.aln")
> >>> al=do_alignment(cline)
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> File "C:\Python25\Lib\site-packages\Bio\Clustalw\__init__.py", line 124,
> in do_alignment
> % command_line.sequence_file)
> IOError: Cannot open sequence file C:\Documents and
> Settings\student\Desktop\Foo\mtr4.fasta
>
> when I open the file using o=open('C:\Documents and
> Settings\student\Desktop\Foo\mtr4.fasta') it woks fine.
>
> any ideas?
As a general tip, try this to see what the command Biopython is trying
to run is:
>>> print cline
Then try running the same command by hand at the command prompt (DOS
prompt), and make sure it works.
I can tell from the error message you have Python 2.5, but what
version of Biopython do you have?
I'm not at a Windows machine to check, but it is generally a good idea
to avoid file names and paths with spaces where you can. In this
case, I'm sure relative names would be fine:
>>> import os
>>> from Bio.Clustalw import MultipleAlignCL
>>> from Bio.Clustalw import do_alignment
>>> cline=MultipleAlignCL("mtr4.fasta", r"C:\Program Files\clustalw1.83.XP\clustalw.exe")
>>> cline.set_output("test.aln")
Peter
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