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

[Eric Gibert]

Dear all,

When I retrieve a BioSQL.BioSeq.DBSeqRecord which was inserted previously by my BioJava application, I have:

print "Debug on Seq:", Seq.id, "=", Seq.annotations.keys()

Debug on Seq: AJ459190.1 = ['ORIGIN', 'DIVISION', 'genbank_accessions', 'TITLE', 'cross_references', 'data_file_division', 'VERSION', 'references', 'KEYWORDS', 'GI', 'SIZE', 'DEFINITION', 'REFERENCE', 'MDAT', 'ORGANISM', 'JOURNAL', 'ACCESSION', 'LOCUS', 'SOURCE', 'PUBMED', 'AUTHORS', 'TYPE', 'CIRCULAR']

but a freshly inserted BioSeq by BioPython 1.44 only gives me:
Debug on Seq: EF631597.1 =  ['cross_references', 'dates', 'references', 'gi', 'data_file_division']


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?

Eric




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