[Biopython-dev] [Bug 2390] Error importing Swiss Prot in BioSQL

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Tue Nov 13 13:07:28 UTC 2007


------- Comment #15 from biopython-bugzilla at maubp.freeserve.co.uk  2007-11-13 08:07 EST -------
I haven't downloaded the 1GB uniprot_sprot.dat file, however using the example
files from biopython/Tests/SwissProt seems to work for me now using CVS:

from BioSQL import BioSeqDatabase
from Bio import SeqIO
import os

server = BioSeqDatabase.open_database(driver='MySQLdb', user='root', passwd='',
host='localhost', db='bioseqdb')
db = server.new_database('bug2390')
for filename in os.listdir(".") :
    if filename[:2]=="sp" :uniprot_sprot.dat
        print "Loading %s" % filename
        db.load(SeqIO.parse(open(filename), "swiss"))

print "Committing..."

The commit issue is covered by bug 2395, so I would like to mark this as fixed.

Jon - could you update your copy of Biopython and re-test?  Thanks

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