[BioPython] small "bug" correction in package BioSql

Peter biopython at maubp.freeserve.co.uk
Thu Nov 8 11:40:00 UTC 2007


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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