[Bioperl-l] problem parsing WU-blast output

Joseph Fass joseph.fass at gmail.com
Wed Oct 24 18:53:41 EDT 2007


I just updated to 1.5.2 via CPAN, and verified that that worked, and re-ran
my code ... same problem: it's still picking up "unfiltered+1" as the first
->next_hit result from wu-blast output.  This is a different issue than the
fixed bug (ID: 1649) I just found on bugzilla; that bug concerned the hit
sequences.  I'll post a report on bugzilla along with some files to try it
with (please let me know if what I upload there is incomplete).

Thanks for the quick attention, all!

~joe




On 10/24/07, Jason Stajich <jason at bioperl.org> wrote:
>
> I'm pretty sure we fixed this problem after 1.4 so current "unstable" code
> a try first and let us know nif that solves the problem.
>
> also - copy+paste of BLAST files on mailing list doesn't work so well so
> either a link to  URL or posting the file in a bugzilla bug (
> bugzilla.open-bio.org) make it easier for someone to try this at home.
>
> -jason
> On Oct 24, 2007, at 5:43 PM, Joseph Fass wrote:
>
> Hi Dave,
>
> here's my code, followed by a sample wu-blast report (below).
> I'm using bioperl version 1.4
> Thanks for looking into it, and I'd be very curious to know what you find.
>
> Joe
>
> [SNIP]
> --
> Jason Stajich
> jason at bioperl.org
>
>


-- 
Joseph Fass
joseph.fass at gmail.com  ||  joefass at hotmail.com
970.227.5928 (c)  ||  530.754.7978 (w)


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