[BioPython] biopython clustalw command line take 2

[Michiel Jan Laurens de Hoon]

ashleigh smythe wrote:
> 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.

Did you try
 >>> help(MultipleAlignCL)

> ... 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
> 
It looks like that should be str(self.gap_open_pen) instead of just 
self.gap_open_pen. If you change that line and similar lines in the 
__init__.py file, it will work.

--Michiel.


-- 
Michiel de Hoon
Assistant Professor
University of Tokyo, Institute of Medical Science
Human Genome Center
4-6-1 Shirokane-dai, Minato-ku
Tokyo 108-8639
Japan
http://bonsai.ims.u-tokyo.ac.jp/~mdehoon