[Biopython-dev] Python 2.6

Peter biopython at maubp.freeserve.co.uk
Mon Oct 13 12:00:08 UTC 2008

> Something the unit tests didn't flag up is the deprecation of popen2,
> os.popen2, os.popen3, and os.popen4 in python 2.6 - see
> http://www.python.org/dev/peps/pep-0361/

Some progress:

Bio.Blast.NCBIStandalone - fixed in CVS, uses subprocess where available
Bio.Application - fixed in CVS, uses subprocess where available

These two changes passed my own hand testing, but as we don't have any
unit tests covering these having a 3rd party double check would be a
good idea.

Bio.Clustalw - actually only uses os.popen which is still OK
Bio.Emboss.Applications - only via Bio.Application, so OK

Leaving just:

Bio.PDB.NACCESS - uses os.popen3, looks simple to update but I don't
have naccess installed yet.  I suppose this would make a nice unit
test too.
See http://www.bioinf.manchester.ac.uk/naccess/


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