[BioPython] Alignment with Emboss water tool

[Stefanie Lück]

Hi!

I'm trying to make an alignment with Emboss water. Here's my code:

from Bio.Emboss.Applications import WaterCommandline
from Bio.Application import generic_run

water = WaterCommandline()
water.set_parameter("-asequence", "asis::atgctccg")
water.set_parameter("-bsequence", "asis::taggcgctcgctcgatgctccgatgctcgc")
water.set_parameter("-gapopen", "10")
water.set_parameter("-gapextend", "0.5")
water.set_parameter("-outfile", "test2.txt")
final = generic_run(water)

I get the following error:

Traceback (most recent call last):
File "C:\Dokumente und Einstellungen\Administrator\Desktop\water.py", line 10, in <module>
final = generic_run(water)
File "C:\Python25\lib\site-packages\Bio\Application\__init__.py", line 18, in generic_run
child = popen2.Popen3(str(commandline), 1)
AttributeError: 'module' object has no attribute 'Popen3'

Does someone knows how to fix this?

Thank in advance!
Stefanie