[Bioperl-l] megablast parsing broken?

[Neil Saunders]

Hi,

I was just trying to use Bio::SearchIO to parse a megablast report, 
without success.  I ran megablast with the "D 2" option which produces 
"traditional" BLAST output.  According to the docs, this should parse as 
for a normal blastn report, but parsing only seems to read data from the 
final hit.  I also tried the megablast.pm module from cvs but this 
extracts nothing at all from the report.

Trawling through the mailing lists, I see this was reported as an issue 
a few months ago.  Any progress since then or anything I am missing?  I 
could post code (but it's just the "while($result...) 
while($hit...)" standard example code.  I have looked at the megablast 
format and it differs from a blastn with multiple queries in that the 
BLAST statistics are all at the end, rather than separating each result 
and misses a few blank lines as compared with blastn.  That's all the 
differences I can see.

thanks,
Neil
-- 
 School of Biotechnology and Biomolecular Sciences,
 The University of New South Wales,
 Sydney 2052,
 Australia

http://psychro.bioinformatics.unsw.edu.au/neil/index.php