[BioPython] Problems runing BLAST

[Peter]

Hi Bruno,

On Jan 29, 2008 11:34 AM, Bruno Santos <bsantos at biocant.pt> wrote:
> I am once more having problems running blast using biopython. I start the
> script the blastall process starts and after a few minutes it starts
> sleeping and no error message is passed. When I check the xml file it only
> writes part of the results for the first sequence.

Have you tried running the same command "by hand" at the command line,
to check that is works, and time how long you should expect it to
take?

> Does anyone has ever had the same problem?

I think the problem is to do with asking the operating system to read
all the error output.  Try commenting out this bit, and only read the
error handle if you have a problem:

# print error_info.read()

Quoting from the tutorial,

>> The error info can be hard to deal with, because if you try to do a
error_handle.read() and
>> there was no error info returned, then the read() call will block
and not return, locking your
>> script. In my opinion, the best way to deal with the error is only
to print it out if you are not
>> getting result_handle results to be parsed, but otherwise to leave it alone.

Peter