[Biopython-dev] [Bug 2502] PSIBlastParser fails with blastpgp 2.2.18 though works with blastpgp 2.2.15

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Fri May 23 07:02:44 EDT 2008


http://bugzilla.open-bio.org/show_bug.cgi?id=2502





------- Comment #6 from biopython-bugzilla at maubp.freeserve.co.uk  2008-05-23 07:02 EST -------
That's an interesting theory - reading directly from standard out is causing
the problem (comment 5).  One thing you could try is writing the blastpgp
output to a file, and then opening the file for reading.

I'm not sure if blastpgp has a file output option.  You could just try this:

blast_out, error_info = NCBIStandalone.blastpgp(...)
handle = open("blastpgp_2.2.18.txt","w")
handle.write(blast_out.read())
handle.close()
blast_out = open("blastpgp_2.2.18.txt")
b_parser = NCBIStandalone.PSIBlastParser()
b_record = b_parser.parse(blast_out)
...

Or, for a very crude workaround:

from time import sleep
blast_out, error_info = NCBIStandalone.blastpgp(...)
sleep(5*60) #Five minutes
b_parser = NCBIStandalone.PSIBlastParser()
b_record = b_parser.parse(blast_out)
...

If those work, it would be good evidence that your theory is right.


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