[Biopython] Clustalw Hangs on Python 2.6
Peter
biopython at maubp.freeserve.co.uk
Fri Apr 24 17:47:24 EDT 2009
On 4/24/09, Marco Gallotta <marco at gallotta.co.za> wrote:
> Hi
>
> I recently upgraded to Python 2.6 (from 2.5) and this seems to have
> revealed a potential bug in biopython. I'm using biopython to run
> clustalw and after the upgrade it just hangs. I discovered that it was
> hanging on a write to stdout. The best reason I could determine for
> this behaviour was that Python's subprocess module (which biopython
> uses to spawn clastlw) was piping stdout to bioypython, which wasn't
> reading it.
Hi,
You didn't say what version of Biopython you are using - Bug 2804 was
fixed in Biopython 1.50 which sounds possibly related:
http://bugzilla.open-bio.org/show_bug.cgi?id=2804
Peter
More information about the Biopython
mailing list