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

[Hilmar Lapp]

It seems BioPerl and Biopython both want (and have traditionally  
used) lowercase - do you mind going with that for Biojava as well, or  
alternatively, simply map upon insert/update and retrieve?

	-hilmar

On Nov 8, 2007, at 11:18 AM, Richard Holland wrote:

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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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-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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