[BioPython] NCBIStandalone.iterator hangs

[David Toomey]

Hi Peter

It is part of a large script that I have written but I have replicated the
problem with the following simple script 

blast_out, error_info = NCBIStandalone.blastall("C:/Program Files/Blast/bin"
, "blastp", "C:/blast_test/new_prot_target_for_download.txt",
"C:/blast_test/problem.txt")
b_parser = NCBIStandalone.BlastParser()
b_iterator = NCBIStandalone.Iterator(blast_out, b_parser)
record = b_iterator.next()
print record.query


I don't get any stack trace. I have tried it from the windows command line,
Komodo and also on a linux box (although the linux box is Python 2.3.3
rather than 2.4)
When I say it hangs I mean it just dosn't return after the b_iterator.next()
statement. There is no error message or stack trace.

I have run the blast manually from the windows command line and it works
fine.
The above script works fine with other fasta query sequences against the
same database.

Cheers,
 
Dave
-----Original Message-----
From: Peter (BioPython List) [mailto:biopython at maubp.freeserve.co.uk] 
Sent: 13 October 2006 16:23
To: David Toomey
Cc: biopython at biopython.org
Subject: Re: [BioPython] NCBIStandalone.iterator hangs

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