def test_v3_seq_id_file_read_warning(self):
with pytest.warns(UserWarning) as record:
Adat.from_file('tests/data/v3_test.adat')
# check that only one warning was raised
self.assertEqual(len(record), 1)
# check that the message matches
self.assertEqual(
record[0].message.args[0],
'V3 style seqIds (i.e., 12345-6_7). Converting to V4 Style. The adat file writer has an option to write using the V3 style'
)
def test_v3_seq_id_file_read_conversion(self):
adat = Adat.from_file('tests/data/v3_test.adat')
# check that the adat has the correct column metadata names and data
self.assertEqual(['SeqId', 'SeqIdVersion', 'ColCheck'],
list(adat.columns.names))
self.assertEqual(['12345-6', '23456-7', '34567-8'],
list(adat.columns.get_level_values('SeqId')))
self.assertEqual(['7', '8', '9'],
list(adat.columns.get_level_values('SeqIdVersion')))
def setUp(self):
self.adat = Adat.from_file('./tests/data/control_data.adat')
def setUp(self):
first_adat = Adat.from_file('./tests/data/control_data.adat')
first_adat.to_file(self.filename)
self.adat = Adat.from_file(self.filename)
def setUp(self):
self.adat = Adat.from_file(self.filename)
def test_adat_from_file_read(self):
adat = Adat.from_file(self.filename)
self.assertIsInstance(adat, Adat)
