[BioPython] os.system problem with clustalw
Peter
biopython at maubp.freeserve.co.uk
Wed Jul 25 14:21:53 UTC 2007
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
More information about the Biopython
mailing list