[Biojava-l] small "bug" correction in package BioSql

[Hilmar Lapp]

Indeed Biojava uses uppercase for alphabet. In Bioperl-db, we  
explicitly lowercase the value found for alphabet, and the comment  
says why:

         # Note: Biojava uses upper-case terms for alphabet, so we
         # need to change to all-lower in case the sequence was
         # manipulated by Biojava.
         $obj->alphabet(lc($rows->[3])) if $rows->[3];

However, when inserting sequences, we leave the value as is in  
BioPerl (which is lowercase), leading to a potential problem for  
Biojava upon retrieval. Do the Biojava folks deal with that? Should  
this may harmonized across the board?

	-hilmar

On Nov 8, 2007, at 6:49 AM, Eric Gibert wrote:

> Dear Peter,
>
> All the alphabet are "DNA" (upper case) in my database. The  
> sequences are taken from NCBI by a BioJava application.
> Thus is should be that BioJava inserts the records with "DNA". Thus  
> no potential "hidden bug" in BioPython.
>
> Maybe a point to share with the Open-Bio committee.
>
> Eric
>
> ----- Message d'origine ----
> De : Peter <biopython at maubp.freeserve.co.uk>
> À : Eric Gibert <ericgibert at yahoo.fr>
> Cc : biopython at lists.open-bio.org
> Envoyé le : Jeudi, 8 Novembre 2007, 19h40mn 00s
> Objet : Re: [BioPython] small "bug" correction in package BioSql
>
> Eric Gibert wrote:
>> Dear all,
>>
>> In BioSeq/BioSeq.py, in the class DBSeq definition, we have the
>> function:
>>
>> ...
>>
>> please note my correction: force moltype to be turn in lower case as
>> my database has upper case value! this raises the "Unknown moltype"
>> error.
>
> Hi Eric, I've made your suggested change in CVS,
> biopython/BioSQL/BioSeq.py revision 1.13, thank you.
>
> I would encourage you to investigate why some of the "alphabet" fields
> in the biosequence table are in upper case.  There could be a bug
> elsewhere which is writing these entries with the wrong alphabet.  Is
> this affecting all entries, or just some?
>
> Peter
>
>
>
>
>
>
>
>        
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-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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