[Bioperl-l] PSI-BLAST parsing fails on Windows

[Chris Fields]

Could you submit this as a bug in Bugzilla so we can track it and  
attach the blast output files if they are small enough?  If Bugzilla  
rejects the files b/c they are too large (I think the cutoff is  
100-200 KB) you can attach them to an email and send them to me  
directly.  I'll try the fix on Mac OS X and Windows, run tests, and  
commit the fix if everything passes.

Chris

On Apr 18, 2006, at 5:05 PM, David Waner wrote:

> I have found that there is a small difference in output format between
> the linux and Windows versions of NCBI blastpgp that causes parsing of
> psi-blast results to fail on Windows.  Specifically, the Windows  
> version
> of blastpgp does not output the "Searching.done" lines between the
> results of each iteration.  For example:
> ---------------------------------------------------------------------- 
> -----------
> LINUX:
>
> Database: C:\BioPerl\REGRES~1\Output\R517_protDB
>            100 sequences; 33,683 total letters
>
> Searching.done
>
>
> Results from round 1
> ---------------------------------------------------------------------- 
> -----------
> WINDOWS:
>
> Database: C:\BioPerl\REGRES~1\Output\R517_protDB
>            100 sequences; 33,683 total letters
>
>
> Results from round 1
> ---------------------------------------------------------------------- 
> -----------
> As a fix I have changed line 474 of Bio::SearchIO::blast.pm
> from:
>     elsif (/^Searching/) {
> to:
>     elsif (/^Results from round/) {
>
> This seems to fix the problem without breaking anything, but I would
> like to see if anyone on the mailing list can run some additional test
> cases, or sees anything wrong with this proposed change before I  
> submit
> it to bugzilla.
>
> Thanks.
>
> - David
>
>
> Additional information:
>
> This problem occurs with blast versions 2.2.10 and 2.2.13.
> I have the latest version of blast.pm (1.92) from the bioperl-live  
> cvs.
>
>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign