[BioPython] NCBIStandalone.iterator hangs

[David Toomey]

Hi

 

I have been writing some scripts which make use of the NCBIStandalone module
and I have found that when I iterate the results from some local blast runs
my script will hang. I have attached 2 examples. I have been running them
against two fasta files from drugbank  
http://redpoll.pharmacy.ualberta.ca/drugbank/download.htm

I have tried them against two of the downloads from this site, the redundant
and non-redundant "drug target protein sequences"

 

The first query sequence (problem.txt) only hangs when run against the non
redundant, the other sequence hangs when run against either. I have tracked
down the line that hangs to "line = self._handle.readline(*args,**keywds)"
in the readline method of Bio.File.UndoHandle

 

I have no idea why this would be happening so any help would be appreciated.
I am using Biopython 1.42, Python 2.4.3 and blast 2.2.13

 

Cheers,

 

Dave

 

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