def test_CreateFromSeqRecord(self):
with GeneSequenceApp.app.test_request_context("/"):
GeneSequenceApp.app.preprocess_request()
with open(__location__ + "/testfiles/422900759.pickle", 'rb') as f:
record = pickle.load(f)
GenBankEntry.create_from_seqrecord(record, "")
entry = Sequence.create_from_seqrecord(record)
self.assertEqual(entry.Sequence, str(record.seq))
def try_add_from_genbank(id, silk_type):
get_module_logger().info("Calling entrez for ID {}".format(id))
fasta = entrez_get_fasta_seqrecord(id)
success = False
if fasta is not None:
get_module_logger().info("Data for ID {} found. Trying to add to database.".format(id))
try:
get_module_logger().info("Creating GenBankEntry.")
GenBankEntry.create_from_seqrecord(fasta, silk_type)
get_module_logger().info("Creating Sequence.")
Sequence.create_from_seqrecord(fasta)
success = True
except:
raise
else:
get_module_logger().info("Data for ID {} not found.")
return success
