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

[Richard Holland]

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we do need a consensus here.

I'm happy to go with whatever value is chosen, as the BioJava code can
easily be modified to suit.

cheers,
Richard

Hilmar Lapp wrote:
> 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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