-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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 <[EMAIL PROTECTED]> >>>>> À : Eric Gibert <[EMAIL PROTECTED]> >>>>> Cc : [EMAIL PROTECTED] >>>>> 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 >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> ______________________________________________________________________ >>>>> _______ >>>>> Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers >>>>> Yahoo! Mail >>>>> _______________________________________________ >>>>> BioPython mailing list - [EMAIL PROTECTED] >>>>> http://lists.open-bio.org/mailman/listinfo/biopython >>>> > --=========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : > =========================================================== -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFHNByl4C5LeMEKA/QRAmCzAJ9fxSm8l5YAEHAUe2hH+Gwc1Xe5IwCfcMf6 c9sy8lASDV069FQJ79Geemw= =RHM1 -----END PGP SIGNATURE----- _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
