[Tutor] how to execute software within python

[Danny Yoo]

On Wed, 28 Aug 2002, biter bilen wrote:

> i am to run clustalw program within python. but the program doesn't
> recognise clustalw. in general in what directory should these kind of
> software be installed to be run within scripts?

Hi Biter,


If you're a bioinformatics sort of person, the Biopython project should be
useful for you.  The latest version of Biopython in CVS has a 'clustalw'
module that may make it easier to work with the software in Python.

(Underneath, it does do an os.popen() as well, but provides other services
like parsing the clustalw report.)


See:

http://www.pasteur.fr/recherche/unites/sis/formation/python/ch11s06.html#sect_clustalw

for more details on driving the clustalw program with Python.  Good luck!