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

Wed Nov 26 06:38:14 EST 2003

Hey Heikki!

Those are great links!  Thanks for the heads-up!

If I produce anything "useful" I will certainly make it public.  We'll
see how the lessons go.  It is going to be a mixture of the SeqHound API
and the BioPerl API, so it isn't 100% BP...

M

On Wed, 2003-11-26 at 01:38, Heikki Lehvaslaiho wrote:
> Mark,
> 
> Did you remember this:
> 	http://www.ebi.ac.uk/~lehvasla/bioperl/
> there is a quite detailed page about using anonymous cvs:
> 	http://www.ebi.ac.uk/~lehvasla/bioperl/InstallingBioperl.html
> 
> We should put that into bioperl website somewhere...
> 
> Are you  going to make your materials available?
> 
> 	-Heikki
> 
> On Tuesday 25 Nov 2003 7:54 pm, Mark Wilkinson wrote:
> > 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