[BioPython] Re : small "bug" correction in package BioSql

[Eric Gibert]

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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