[BioPython] Help getting GenBank data into Database

Andreas Kuntzagk andreas.kuntzagk@mdc-berlin.de
Mon, 27 May 2002 13:21:42 +0200


Hello,

i'm trying to get the Data from a GenBank flatfile into the mySql 
database. I've got biopython from cvs. I created all the tables
whith the bioSQL schema and created an new biodatabase.

Then I try the following:
----
from Bio import GenBank
from BioSQL import BioSeqDatabase

database = BioSeqDatabase.open_database(db="test")
f=open("/home/kuntzagk/gb_1.dat","r")
parser = GenBank.RecordParser()
it = GenBank.Iterator(f,parser)
biodata = BioSeqDatabase.BioSeqDatabase(database.adaptor, "test")
biodata.load(it)
---

the last Command gives me an Error:

Traceback (most recent call last):
   File "load_database.py", line 9, in ?
     biodata.load(it)
   File 
"/home/kuntzagk/lib/python2.2/site-packages/BioSQL/BioSeqDatabase.py", 
line 276, in load
     db_loader.load_seqrecord(cur_record)
   File "/home/kuntzagk/lib/python2.2/site-packages/BioSQL/Loader.py", 
line 28, in load_seqrecord
     bioentry_id = self._load_bioentry_table(record)
   File "/home/kuntzagk/lib/python2.2/site-packages/BioSQL/Loader.py", 
line 68, in _load_bioentry_table
     accession, version = record.id.split('.')

What is wrong ?

Thanx, Murple