[Biopython] Clustalw Hangs on Python 2.6

[Peter]

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