[BioPython] Problem with standalone BLAST

[Brad Chapman]

Hi Andreas;

> I'm having problems with the "NCBIStandalone.blastall".
> After launching the Blast with "doBlast" it runs for a while and then starts
> to sleep. However, it never awakes from this state.

Could you post a minimal example that demonstrates the problem? This
will help us try and narrow things down -- whether it be something
in Biopython, the code that you are writing, BLAST itself, the
platform, or whatever. Otherwise we can only really guess what the
problem might be. For instance, the following simple example
works fine for me on my system:

from Bio.Blast import NCBIStandalone

output, error = NCBIStandalone.blastall("/usr/local/bin/blastall",
                  "blastp", "input.fasta", "database.fasta")
print output.readline()

Does something this simple show the problem you are seeing? If you
can break it down to a simple example hopefully we can get it fixed
up.

Thanks much!
Brad