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

[David Waner]

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.