[BioPython] biopython clustalw command line take 2

[ashleigh smythe]

Hello biopython experts.  At the risk of seeming like a pest, I'm
reposting a question I asked a couple of days ago to see if I can get a
bite this time.

I'm trying to use clustalw through biopython for the first
time.  I'm following the tutorial but it doesn't show the syntax for
setting the multiple alignment parameters.  From the __init__ I figured
out that it is something like gap_open_pen=desired value so I tried
cline.gap_open_pen=20 but when I try to show that command line string I
get an error:

>>> cline=MultipleAlignCL(os.path.join(os.curdir, 'aligntest'))
>>> cline.set_output('alignout.aln')
>>> cline.gap_open_pen=20
>>> cline.gap_ext_pen=10
>>> str(cline)
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "/usr/lib/python2.2/site-packages/Bio/Clustalw/__init__.py", line
420, in __str__
    cline = cline + " -GAPOPEN=" + self.gap_open_pen
TypeError: cannot concatenate 'str' and 'int' objects

How do I set those values properly?

Thanks very much for any suggestions.

Ashleigh
-- 
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Ashleigh B. Smythe
Graduate Research Assistant
Department of Nematology
University of California,
Davis, CA 95616
email:absmythe at ucdavis.edu
phone:530-754-4321

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