[Biopython-dev] 5/13 BioStar - Biopython Questions

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1. Clustalw alignment problem
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May 12, 2010 at 4:54 PM

Hi everyone,

I tried these lines 

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import os
from Bio.Clustalw import MultipleAlignCL

cline = MultipleAlignCL(os.path.join(os.curdir, "opuntia.fasta"))

cline.set_output("test.aln")

alignment = Clustalw.do_alignment(cline)


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But couldn't proceed with these errors

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Traceback (most recent call last):

  File "<string>", line 244, in run_nodebug

  File "C:\Python24\align.py", line 5, in ?

    alignment = Clustalw.do_alignment(cline)

  File "C:\Python24\lib\site-packages\Bio\Clustalw\__init__.py", line 95, in do_alignment

    shell=(sys.platform!="win32")

  File "C:\Python24\lib\subprocess.py", line 534, in __init__

    (p2cread, p2cwrite,

  File "C:\Python24\lib\subprocess.py", line 594, in _get_handles

    p2cread = self._make_inheritable(p2cread)

  File "C:\Python24\lib\subprocess.py", line 635, in _make_inheritable

    DUPLICATE_SAME_ACCESS)

TypeError: an integer is required


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test.aln is not generated too

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Thanks

http://biostar.stackexchange.com/questions/1041/clustalw-alignment-problem

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