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

[Richard Holland]

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i'll see what i can do.

Hilmar Lapp wrote:
> 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:
> 
> 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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>>>>

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






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