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

Jason Stajich jason at bioperl.org
Fri Apr 13 16:13:07 EDT 2007


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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