[BioPython] biopython clustalw command line question

[ashleigh smythe]

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