[BioPython] Blast parser problem

[Jeffrey Chang]

On Thu, Jun 20, 2002 at 02:30:24PM +0200, Karl Schmid wrote:
> When I run Blast from a python script, the Biopython blast parser gets
> stuck during the parsing of the HSPs. Killing the process (on LInux):
> gives the following output:

By stuck, do you mean that this process runs for an unreasonable
amount of time and needs to be killed?  I'm not sure what could be
causing that.  From the traceback, it looks like it's blocking on a
read from the process.

[traceback cut]

> Interestingly, when I do the blast manually with the following command:
> 
> schmid@blossom:~/work/xan> blastall -p blastp -d xac -i yapH.fas >
> blast.out

What happens when you try to parse "blast.out"?  Does the parsing
finish, give a traceback, or still require killing?

Jeff