[Bioperl-l] SearchIO and bl2seq blast reports
billk at iinet.net.au
Tue Nov 30 02:33:47 EST 2004
Filed as bug 1713 with the bl2seq blastn report as an attachment
On Mon, 2004-11-29 at 22:58 -0500, Jason Stajich wrote:
> Should work - we have tests in the bioperl-live code for strandedness
> and bl2seq reports for blastn and tblastn.
> in t/SearchIO.t
> ok($hsp->query->start, 94);
> ok($hsp->query->end, 180);
> ok($hsp->query->strand, 1);
> ok($hsp->hit->strand, -1);
> ok($hsp->hit->start, 1);
> I don't remember if this bug was fixed before 1.4 went out but
> SearchIO::blast parsing was definitely updated for several bugs since
> 1.4.0 release.
> Can you post a report and exact code that you are testing as a bug
> report to http://bugzilla.open-bio.org and someone can have a looksie.
> On Nov 29, 2004, at 8:04 PM, Bill Kenworthy wrote:
> > Hi, what is the best way to detect strandedness using SearchIO parsing
> > bl2seq reports? Or should I go back to BPLite which I think works.
> > There were bugs posted about this in the past, but SearchIO in 1.4 is
> > still returning 0 for frame and strand on both hit and query with any
> > form of bl2seq I have tried.
> > BillK
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> Jason Stajich
> jason.stajich at duke.edu
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
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