[BioPython] NCBIStandalone.iterator hangs

[Peter (BioPython List)]

Hi David

David Toomey wrote:
> 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.

When you say the first query sequence (problem.txt) "hangs" do you get a 
python stack trace?

What is the script you are using?  I'm going to guess that you are using 
python to invoke the NCBI standalone blast program.

Have you tried running standalone blast "by hand" at the command line, 
and had a look at the output?

Are you getting plain text output or XML from the blast program?

> I am using Biopython 1.42, Python 2.4.3 and blast 2.2.13

On Windows, Linux or Mac OS X?

Peter