-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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 > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFHMzbm4C5LeMEKA/QRAtzGAJ98MKWg0uUOafDVVkihSzfSTwtfxACgi6q3 9x+CUHig3GfBCZ56rDb1ZG4= =OJyB -----END PGP SIGNATURE----- _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
