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

Tue Nov 25 13:24:21 EST 2003

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