[BioPerl] Re: [Bioperl-l] Bio::Perl blast function not working?

Tue Nov 25 14:54:37 EST 2003

Yup - switching to the CVS version solved the problem.  I'll just change
my lesson to teach the students how to use CVS first, and then get them
to install BioPerl from CVS instead of CPAN or downloading the latest
dist.

Cheers!

Mark

On Tue, 2003-11-25 at 12:24, Jason Stajich wrote:
> You may need to use bioperl 1.3.x - as per the other posts which describe
> the problems - 1.2.x did not handle NCBI WebBlast changes which appended
> stuff to the RID line.  Or just change the regexep in
> Tools::Run::RemoteBlast as others have described.
> 
> -jason
> 
> On Tue, 25 Nov 2003, Mark Wilkinson wrote:
> 
> > Yup, so long as i know that it is still a going concern I will have a
> > look at it myself to see if i can track it down.
> >
> > The bug can be reproduced as follows:
> >
> > use Bio::Perl;
> >
> > $seq = get_sequence('swissprot', 'P35632');
> > $blast = blast_sequence($seq);
> > write_blast(">mySequenceBlast", $blast);
> >
> >
> > results in:
> >
> > Submitted Blast for [AP3_ARATH]
> > -------------------- WARNING ---------------------
> > MSG:
> >
> > <p><!--
> > QBlastInfoBegin
> > 	Status=UNKNOWN
> > QBlastInfoEnd
> > --><p><BODY BGCOLOR="#FFFFFF">
> > <hr><font color="red">ERROR: Results for RID 1069780799-8428-65894659018
> > not found</font><hr>
> >
> >
> > ---------------------------------------------------
> >
> >
> > I'll have a go at stepping through the code later today after I finish
> > writing this lesson.
> >
> > Cheers all!
> >
> > M
> >
> >
> > On Tue, 2003-11-25 at 10:49, Jason Stajich wrote:
> > > Error messages, your own debugging efforts are always helpful here too...
> > >
> > > -jason
> > > On Tue, 25 Nov 2003, Mark Wilkinson wrote:
> > >
> > > > Hi all,
> > > >
> > > > I'm teaching a course on BioPerl next week and I'm putting the
> > > > "beginners" lesson together using the Bio::Perl module.  I notice that
> > > > the blast_sequence function is not working anymore...  is this just a
> > > > temporary glitch, or is this function not supported these days?
> > > >
> > > > Any advice appreciated,
> > > >
> > > > M
> > > >
> > > >
> > > >
> > >
> > > --
> > > Jason Stajich
> > > Duke University
> > > jason at cgt.mc.duke.edu
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at portal.open-bio.org
> > > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
> 
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
-- 
Mark Wilkinson <markw at illuminae.com>
Illuminae