[BioPython] NCBIStandalone.iterator hangs

[David Toomey]

Thanks for the help Peter

The attached file has the output from two queries, problem.txt and
works.txt, when run manually from the command line


I also edited the NCBIStandalone module to add a print statement to
Iterator.next() and then ran the same two files using the script. 
If you compare the two reports for problem.txt you can see on which line of
the report the iterator is hanging. I have had a look at this and can't see
anything about the line that is unusual?

The last line outputted by the script is 
Query: 266 LAAHIDQYDIDAMTGIRATDIEKTDEAIKVTLENGAVLESKTVIIATGAGWRKLNIPGEE 325


And the manual report continues with
               I    +          +       ++  +   VL                      
Sbjct: 68  GIMSIPTLILFKGGE-PVKQLIGYQPKEQLEAQLADVL-                      125



Even though problem.txt generates a valid report when run manually it does
output a load of errors of the type below, but I am not sure how this would
cause the script to stop at the line above. 

[NULL_Caption] ERROR: ncbiapi [000.000]  AHPF_STAAC: SeqPortNew:
lcl|EXPT02286 s
top(365) >= len(329)
[NULL_Caption] ERROR: ncbiapi [000.000]  AHPF_STAAC: SeqPortNew:
lcl|EXPT02286 s
top(336) >= len(329)
[NULL_Caption] ERROR: ncbiapi [000.000]  AHPF_STAAC: SeqPortNew:
lcl|EXPT02286 s
tart(337) >= len(329)
[NULL_Caption] ERROR: ncbiapi [000.000]  AHPF_STAAC: SeqPortNew:
lcl|EXPT02286 s
tart(338) >= len(329)
[NULL_Caption] ERROR: ncbiapi [000.000]  AHPF_STAAC: SeqPortNew:
lcl|EXPT02113 s
tart(284) >= len(149)


If it is easier for you I can certainly raise a bug, I just wanted to be
sure it wasn't anything silly that I was doing before I did this.


Cheers,
 
Dave

-----Original Message-----
From: Peter [mailto:biopython at maubp.freeserve.co.uk] 
Sent: 16 October 2006 12:11
To: David Toomey
Subject: Re: [BioPython] NCBIStandalone.iterator hangs

David Toomey wrote:
> Hi Peter
> 
> It is part of a large script that I have written but I have 
> replicated the problem with the following simple script

Thank you.

> 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.

That fact that the script runs fine on other query sequences is 
important.  My guess is that the output for problem.txt is somehow 
different (maybe no matches), and the parser can't cope.

Could you email me the blast output from using problem.txt as input, and 
a second working output from a different query?  Or, if you would 
rather, file a bug and attach the two output files to it.

You could do this from the command line, or using python save the 
blast_out text generated by NCBIStandalone.blastall to a file.

(Looking back over the emails, I can't see what version of NCBI 
Standalone BLAST you have - but it should be specified in the blast output.)

Thanks

Peter


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