[BioPython] os.system problem with clustalw

[Peter]

Emanuel Hey wrote:
> Thanks much for responding
> 
> ok,  I had no idea Clustalw was so particular about its command line
> flags.

Its confused me in the past too!

> I was not using Bio.Clustalw to build the command line because I
> could not get that to work either.

Ahh. Good point. I guess I should have checked this when I wrote my last
email, but it turns out Bio.Clustalw was building it's command lines
without using the INPUT argument... which I've just fixed in CVS.

This should now work:

from Bio.Clustalw import MultipleAlignCL, do_alignment
faa_filename = 'C:\\temp\\pythonplay\\hcgplay\\data.faa'
cline = MultipleAlignCL(faa_filename)
#print cline
align = do_alignment(cline)
for col_index in range(align.get_alignment_length()) :
     print align.get_column(col_index)

Please try this by backing up and then updating the file
Bio/Clustalw/__init__.py to CVS revision 1.15, which you can download here:

http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/Clustalw/__init__.py?cvsroot=biopython

Thanks

Peter