[BioPython] Clustalw Problems

[Bradley Hintze]

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?

--
Bradley


-- 
Bradley J. Hintze
Biochemistry Undergraduate
Utah State University
801-712-8799