[Bioperl-l] megablast parsing broken?

[Jason Stajich]

Do the test files t/data/503384.MEGABLAST.2 & t/data/503384.MEGABLAST.0
parse for you okay if you run them through your script?

This is what is tested and they seem to work fine with both D=0 and D=2
reports.

-jason

On Wed, 23 Apr 2003, Neil Saunders wrote:

> 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
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu