AW: [BioPython] Problem with standalone BLAST

[Andreas Schlicker]

Hi Brad; hi all;

Here is the code I use:

from Bio.Blast import NCBIStandalone

results, errors = NCBIStandalone.blastall(os.path.join(self.dir, blastall'),
program, database, query, expectation = self.e)
save = file(output, 'w')
while 1:
     line = results.readline()
     if not line:
         break
     save.write(line)
results.close()
errors.close()
save.close()

Basically, just run Blast and save it's output to a file. 

Most times this works fine but sometimes Blast does not finish. The process
stays alive but is sleeping after a while and never continues.
I tested it on these two different platforms:

SunOS 5.9
Python 2.3.3
BioPython 1.24

2 x 3.06 GHz Xeon / 4 GByte RAM
RedHat 7.3
Python-2.3.4
Numerical Python 23.1
mxTextTools 2.0.5
reportlab 1.19
Biopython 1.30

To me it looks like a problem with Python because running Blast from the
command line with the same command -- as generated from Biopython -- works
perfect. 

Has anyone had similar problems? Or can think of a solution?
Thanks for your help.
Andreas