def trans(self, filename, format):
original_records = list(SeqIO.parse(open(filename, "rU"), format))
# now open a connection to load the database
server = BioSeqDatabase.open_database(driver = DBDRIVER,
user = DBUSER, passwd = DBPASSWD,
host = DBHOST, db = TESTDB)
db_name = "test_trans1_%s" % filename # new namespace!
db = server.new_database(db_name)
count = db.load(original_records)
self.assertEqual(count, len(original_records))
server.commit()
#Now read them back...
biosql_records = [db.lookup(name=rec.name)
for rec in original_records]
#And check they agree
self.assertTrue(compare_records(original_records, biosql_records))
#Now write to a second name space...
db_name = "test_trans2_%s" % filename # new namespace!
db = server.new_database(db_name)
count = db.load(biosql_records)
self.assertEqual(count, len(original_records))
#Now read them back again,
biosql_records2 = [db.lookup(name=rec.name)
for rec in original_records]
#And check they also agree
self.assertTrue(compare_records(original_records, biosql_records2))
#Done
server.close()
def trans(self, filename, format):
original_records = list(SeqIO.parse(filename, format))
# now open a connection to load the database
server = BioSeqDatabase.open_database(driver=DBDRIVER,
user=DBUSER,
passwd=DBPASSWD,
host=DBHOST,
db=TESTDB)
db_name = "test_trans1_%s" % filename # new namespace!
db = server.new_database(db_name)
count = db.load(original_records)
self.assertEqual(count, len(original_records))
server.commit()
# Now read them back...
biosql_records = [db.lookup(name=rec.name) for rec in original_records]
# And check they agree
self.assertTrue(compare_records(original_records, biosql_records))
# Now write to a second name space...
db_name = "test_trans2_%s" % filename # new namespace!
db = server.new_database(db_name)
count = db.load(biosql_records)
self.assertEqual(count, len(original_records))
# Now read them back again,
biosql_records2 = [
db.lookup(name=rec.name) for rec in original_records
]
# And check they also agree
self.assertTrue(compare_records(original_records, biosql_records2))
# Done
server.close()
def loop(self, filename, format):
original_records = list(SeqIO.parse(open(filename, "rU"), format))
# now open a connection to load the database
server = BioSeqDatabase.open_database(driver = DBDRIVER,
user = DBUSER, passwd = DBPASSWD,
host = DBHOST, db = TESTDB)
db_name = "test_loop_%s" % filename # new namespace!
db = server.new_database(db_name)
count = db.load(original_records)
self.assertEqual(count, len(original_records))
server.commit()
#Now read them back...
biosql_records = [db.lookup(name=rec.name)
for rec in original_records]
#And check they agree
self.assertTrue(compare_records(original_records, biosql_records))
#Now write to a handle...
handle = StringIO()
SeqIO.write(biosql_records, handle, "gb")
#Now read them back...
handle.seek(0)
new_records = list(SeqIO.parse(handle, "gb"))
#And check they still agree
self.assertEqual(len(new_records), len(original_records))
for old, new in zip(original_records, new_records):
#TODO - remove this hack because we don't yet write these (yet):
for key in ["comment", "references", "db_source"]:
if key in old.annotations and key not in new.annotations:
del old.annotations[key]
self.assertTrue(compare_record(old, new))
#Done
server.close()
def loop(self, filename, format):
original_records = list(SeqIO.parse(filename, format))
# now open a connection to load the database
server = BioSeqDatabase.open_database(driver=DBDRIVER,
user=DBUSER,
passwd=DBPASSWD,
host=DBHOST,
db=TESTDB)
db_name = "test_loop_%s" % filename # new namespace!
db = server.new_database(db_name)
count = db.load(original_records)
self.assertEqual(count, len(original_records))
server.commit()
# Now read them back...
biosql_records = [db.lookup(name=rec.name) for rec in original_records]
# And check they agree
self.assertTrue(compare_records(original_records, biosql_records))
# Now write to a handle...
handle = StringIO()
SeqIO.write(biosql_records, handle, "gb")
# Now read them back...
handle.seek(0)
new_records = list(SeqIO.parse(handle, "gb"))
# And check they still agree
self.assertEqual(len(new_records), len(original_records))
for old, new in zip(original_records, new_records):
# TODO - remove this hack because we don't yet write these (yet):
for key in ["comment", "references", "db_source"]:
if key in old.annotations and key not in new.annotations:
del old.annotations[key]
self.assertTrue(compare_record(old, new))
# Done
handle.close()
server.close()
