[Bioperl-l] megablast parsing broken?

[Jason Stajich]

Neil - I've committed some changes which seem to fix the problem.  Not
sure how I missed this before.  Changes are committed in CVS to both the
main trunk and branch depending on what you are tracking.  If you can't
grab things from CVS I can send you a patch compared to the 1.2.1 release
or you can just grab the blast.pm file and plop it into your distro.  Only
Bio/SearchIO/blast.pm needed to be changed for this fix.

Let us know if it fixes things for you.

-jason


On Thu, 24 Apr 2003, Neil Saunders wrote:

> > 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.
>
> Thanks for the tip.
>
> I don't have the .0 file in my distribution (I have 1.2.1), but my
> script worked fine on the D=2 file.
>
> The only difference I can see is that the t/data output file is from
> MEGABLAST 2.2.4 and I am using 2.2.5.  Could this be the problem?
>
> Neil
>

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