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

Tue Nov 25 12:22:34 EST 2003

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
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> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
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-- 
Mark Wilkinson <markw at illuminae.com>
Illuminae