[BioPython] error on insert new sequences from GenBank: no annotations saved in BioSQL database

Peter biopython at maubp.freeserve.co.uk
Thu Nov 8 19:18:47 UTC 2007


Eric Gibert wrote:
> Once I look in the table bioentry_qualifier_value
> 
> * 20 records for a Sequence imported by BioJava
> * 1 only for a Sequence inserted by BioPython: the date which should be inserted by "_load_bioentry_date" in BioSQL/Loader.py
> 
> Quite a few annotations missing, no? 
> 
> Any idea?

So Biopython is recording nothing in table bioentry_qualifier_value 
(apart from the date), but is recording other essential things (in other 
tables) like the sequence itself?

Could you double check your schema, as from the issue I filed as bug 
2394 based on your earlier email, your schema doesn't seem to be up to date:

http://bugzilla.open-bio.org/show_bug.cgi?id=2394

Peter




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