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

Chris Fields cjfields at uiuc.edu
Wed Apr 11 10:44:27 EDT 2007


We could ignore this post... oh the irony!  ;>

It has nothing to do with ignoring you.  Read this:

http://en.wikipedia.org/wiki/Warnock's_Dilemma

Basically your question probably fell on deaf ears b/c no one has  
time to look into it and post a fix.  Realize that BioPerl is, for  
the large part, a volunteer effort and we all have $jobs to worry  
about.  If you want you are more than welcome to file a bug on this  
(if it isn't already filed), which is the best way to make sure  
something is done:

http://www.bioperl.org/wiki/Bugs
http://bugzilla.open-bio.org/

chris


On Apr 11, 2007, at 8:32 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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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign






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