[Bioperl-l] problem parsing WU-blast output

Joseph Fass joseph.fass at gmail.com
Wed Oct 24 19:25:50 EDT 2007


There's a script and sample input file to demonstrate this in Bugzilla, bug#
2388 <http://bugzilla.open-bio.org/show_bug.cgi?id=2388>

~joe



On 10/24/07, Joseph Fass <joseph.fass at gmail.com> wrote:
>
> 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)
>



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


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