[Bioperl-l] rpsblast results unsupported by Bio::SearchIO::Writer

Emeric Sevin emeric.sevin at univ-rennes1.fr
Thu Apr 26 04:48:37 EDT 2007


hi! sorry for the delay, took a little vacation ;-)

indeed I don't see any trouble in coding a supplementary test, I'm just 
not at all familiar with the patch release/bioperl package update and 
would prefer leave that to you. For that purpouse I'll take care of 
that bug post in the coming hours!
Thank you very much
Emeric

Le 13 avr. 07, à 22:13, Jason Stajich a écrit :

> I think it just needs an edit the code in the to_string which checks
> for the type of algorithm.  You'd need to add to the if/elsif cascade
> and add something for the RPSBLAST type and codes the query and
> target dbs and query and target sequence types properly.  This would
> be very trivial to code in, have you tried adding this to see if it
> works?
>
> if you submit a bug with and example report we'd be able to make
> appropriate changes faster.
>
> -jason
> On Apr 11, 2007, at 6:32 AM, Emeric Sevin wrote:
>
>> Hi everybody,
>>
>> I'm sorry to bug, but either I missed something so obvious nobody
>> bothered to answer, either I'm being a little boycotted here...
>> A little help would be very much appreciated
>>
>> Le 22 mars 07, à 16:07, Emeric Sevin a écrit :
>>
>>> Hello,
>>>
>>> I am new to this community, and apologize if this subject has been
>>> posted before.
>>>
>>> I want to print out only selected results from a multiple blast-
>>> alignments results file. Problem is, the algorithm used is
>>> rpsblast. The parsing (with Bio::SearchIO) goes fine, but the
>>> actual writing task yields "unclean" warnings. Although an ouput
>>> is actually written, the writer
>>> (Bio::SearchIO::Writer::TextResultWriter) seems to be disturbed by
>>> the fact rpsblast DBs are not labeled with
>>> "protein"/"nucleic"/"translated".
>>> Does anybody know of an easy fix to that bug, or of another way to
>>> come around it?
>>>
>>> Thank you very much
>>>
>>> Emeric SEVIN
>>> Université de Rennes 1_______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> _______________________________________________
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>
> --
> Jason Stajich
> jason at bioperl.org
> http://jason.open-bio.org/
>
>
>
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