[Biojava-l] small "bug" correction in package BioSql
hlapp at gmx.net
Thu Nov 8 15:53:03 UTC 2007
Indeed Biojava uses uppercase for alphabet. In Bioperl-db, we
explicitly lowercase the value found for alphabet, and the comment
# 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->)) if $rows->;
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?
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.
> ----- 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
>> please note my correction: force moltype to be turn in lower case as
>> my database has upper case value! this raises the "Unknown moltype"
> 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?
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