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

Tue Nov 25 13:08:06 EST 2003

This looks like the same problem that everyone had a month or so ago 
with parsing the RID line (NCBI added a .BLASTQ3 to the end.

Lots of solutions were offered, basically adding (\S+) to the end of 
the line that parses RID should fix it.

Rob

On Tuesday, November 25, 2003, at 11:22  AM, 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
> -- 
> Mark Wilkinson <markw at illuminae.com>
> Illuminae
>
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