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

Wed Nov 26 02:38:21 EST 2003

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

-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________