def setUp(self):
rfu_data = [[1, 2, 3], [4, 5, 6]]
col_metadata = {
'SeqId': ['A', 'B', 'C'],
'SeqIdVersion': ['1', '2', '3'],
'ColCheck': ['PASS', 'FLAG', 'FLAG']
}
row_metadata = {
'PlateId': ['P0012345', 'P0012345'],
'Barcode': ['SL1234', 'SL1235']
}
header_metadata = {}
self.adat0 = Adat.from_features(rfu_data, row_metadata, col_metadata,
header_metadata)
rfu_data = [[5, 6, 7], [6, 5, 4]]
col_metadata = {
'SeqId': ['A', 'B', 'C'],
'SeqIdVersion': ['1', '2', '3'],
'ColCheck': ['PASS', 'PASS', 'FLAG']
}
row_metadata = {
'PlateId': ['Set 01', 'Set 02'],
'Barcode': ['SL1236', 'SL1237']
}
header_metadata = {}
self.adat1 = Adat.from_features(rfu_data, row_metadata, col_metadata,
header_metadata)
def setUp(self):
rfu_data = [[1, 2, 3], [4, 5, 6]]
col_metadata = {
'SeqId': ['A', 'B', 'C'],
'SeqIdVersion': ['1', '2', '3'],
'ColCheck': ['PASS', 'FLAG', 'FLAG']
}
row_metadata = {
'PlateId': ['A12', 'A12'],
'Barcode': ['SL1234', 'SL1235']
}
header_metadata = {
'AdatId': '1a2b3c',
'!AssayRobot': 'Tecan1, Tecan2',
'RunNotes': 'run note 1'
}
self.adat0 = Adat.from_features(rfu_data, row_metadata, col_metadata,
header_metadata)
rfu_data = [[5, 6, 7], [6, 5, 4]]
col_metadata = {
'SeqId': ['A', 'B', 'C'],
'SeqIdVersion': ['1', '2', '3'],
'ColCheck': ['PASS', 'PASS', 'FLAG']
}
row_metadata = {
'PlateId': ['A13', 'A13'],
'Barcode': ['SL1236', 'SL1237'],
'HybControlNormScale': ['1.2', '5'],
'RowCheck': ['PASS', 'PASS']
}
header_metadata = {
'AdatId': '1a2b3d',
'!AssayRobot': 'Tecan2',
'RunNotes': 'run note 2'
}
self.adat1 = Adat.from_features(rfu_data, row_metadata, col_metadata,
header_metadata)
rfu_data = [[8, 9, 1], [1, 4, 8]]
col_metadata = {
'SeqId': ['A', 'B', 'C'],
'SeqIdVersion': ['1', '2', '3']
}
row_metadata = {
'PlateId': ['A14', 'A14'],
'Barcode': ['SL1238', 'SL1239'],
'Stuff': ['foo', 'bar']
}
header_metadata = {
'AdatId': '1a2b3d',
'!AssayRobot': 'Tecan2',
'RunNotes': 'run note 2'
}
self.adat2 = Adat.from_features(rfu_data, row_metadata, col_metadata,
header_metadata)
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 setUp(self):
rfu_data = [[1, 2, 3], [4, 5, 6]]
col_metadata = {'SeqId': ['A', 'B', 'C'], 'ColCheck': ['PASS', 'FLAG', 'FLAG']}
row_metadata = {'PlateId': ['A12', 'A12'], 'Barcode': ['SL1234', 'SL1235']}
header_metadata = {'AdatId': '1a2b3c', '!AssayRobot': 'Tecan1, Tecan2', 'RunNotes': 'run note 1'}
adat1 = Adat.from_features(rfu_data, row_metadata, col_metadata, header_metadata)
rfu_data = [[5, 6, 7], [6, 5, 4]]
col_metadata = {'SeqId': ['A', 'B', 'C'], 'ColCheck': ['PASS', 'PASS', 'FLAG']}
row_metadata = {'PlateId': ['A13', 'A13'], 'Barcode': ['SL1236', 'SL1237']}
header_metadata = {'AdatId': '1a2b3d', '!AssayRobot': 'Tecan2', 'RunNotes': 'run note 2'}
adat2 = Adat.from_features(rfu_data, row_metadata, col_metadata, header_metadata)
self.adats = [adat1, adat2]
def test_column_mismatch(self):
rfu_data = [[5, 6, 7], [6, 5, 4]]
col_metadata = {'SeqId': ['A', 'B', 'D'], 'ColCheck': ['PASS', 'PASS', 'FLAG']}
row_metadata = {'PlateId': ['A13', 'A13'], 'Barcode': ['SL1236', 'SL1237']}
header_metadata = {'AdatId': '1a2b3d', '!AssayRobot': 'Tecan2', 'RunNotes': 'run note 2'}
adat3 = Adat.from_features(rfu_data, row_metadata, col_metadata, header_metadata)
self.adats.append(adat3)
self.assertRaises(AdatConcatError, concatenate_adats, self.adats)
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):
rfu_data = [[1, 2, 3], [4, 5, 6]]
col_metadata = {'SeqId': ['A', 'B', 'C'], 'SeqIdVersion': ['1', '2', '3'], 'ColCheck': ['PASS', 'FLAG', 'FLAG']}
row_metadata = {'PlateId': ['A12', 'A12'], 'Barcode': ['SL1234', 'SL1235'], 'NewColumn': ['1', '2']}
header_metadata = {'AdatId': '1a2b3c', '!AssayRobot': 'Tecan1, Tecan2', 'RunNotes': 'run note 1', '!Title': 'stuff'}
self.adat0 = Adat.from_features(rfu_data, row_metadata, col_metadata, header_metadata)
rfu_data = [[5, 6, 7], [6, 5, 4]]
col_metadata = {'SeqId': ['A', 'B', 'D'], 'SeqIdVersion': ['1', '2', '3'], 'ColCheck': ['PASS', 'PASS', 'FLAG']}
row_metadata = {'PlateId': ['A13', 'A13'], 'Barcode': ['SL1236', 'SL1237'], 'RowCheck': ['PASS', 'FLAG']}
header_metadata = {'AdatId': '1a2b3d', '!AssayRobot': 'Tecan2', 'RunNotes': 'run note 2', '!Title': 'morestuff'}
self.adat1 = Adat.from_features(rfu_data, row_metadata, col_metadata, header_metadata)
rfu_data = [[8, 9, 1], [1, 4, 8]]
col_metadata = {'SeqId': ['A', 'D', 'E'], 'SeqIdVersion': ['1', '2', '3']}
row_metadata = {'PlateId': ['A14', 'A14'], 'Barcode': ['SL1238', 'SL1239']}
header_metadata = {'AdatId': '1a2b3d', '!AssayRobot': 'Tecan2', 'RunNotes': 'run note 2', '!Title': 'evenmorestuff'}
self.adat2 = Adat.from_features(rfu_data, row_metadata, col_metadata, header_metadata)
rfu_data = [[12, 23, 34], [45, 56, 67]]
col_metadata = {'SeqId': ['A', 'B', 'C'], 'SeqIdVersion': ['2', '3', '4'], 'ColCheck': ['PASS', 'FLAG', 'FLAG']}
row_metadata = {'PlateId': ['A12', 'A12'], 'Barcode': ['SL1234', 'SL1235']}
header_metadata = {'AdatId': '1a2b3d', '!AssayRobot': 'Tecan2', 'RunNotes': 'run note 2', '!Title': 'whatstuff'}
self.adat0a = Adat.from_features(rfu_data, row_metadata, col_metadata, header_metadata)
def setUp(self):
rfu_data = [[1, 2, 3], [4, 5, 6]]
col_metadata = {
'SeqId': ['A', 'B', 'C'],
'SeqIdVersion': ['1', '2', '3'],
'ColCheck': ['PASS', 'FLAG', 'FLAG']
}
row_metadata = {
'PlateId': ['A12', 'A12'],
'Barcode': ['SL1234', 'SL1235']
}
header_metadata = {
'AdatId': '1a2b3c',
'!AssayRobot': 'Tecan1, Tecan2',
'RunNotes': 'run note 1'
}
self.adat = Adat.from_features(rfu_data, row_metadata, col_metadata,
header_metadata)
def setUp(self):
rfu_data = [[1, 2, 3], [4, 5, 6]]
col_metadata = {
'SeqId': ['12345-6_7', '23456-7_8', '34567-8_9'],
'ColCheck': ['PASS', 'FLAG', 'FLAG']
}
row_metadata = {
'PlateId': ['A12', 'A12'],
'Barcode': ['SL1234', 'SL1235']
}
header_metadata = {
'AdatId': '1a2b3c',
'!AssayRobot': 'Tecan1, Tecan2',
'RunNotes': 'run note 1'
}
adat = Adat.from_features(rfu_data, row_metadata, col_metadata,
header_metadata)
adat.to_file('tests/data/v3_test.adat')
def test_seq_ids_mismatch_error(self):
rfu_data = [[5, 6, 7], [6, 5, 4]]
col_metadata = {
'SeqId': ['A', 'B', 'D'],
'SeqIdVersion': ['4', '5', '6'],
'ColCheck': ['PASS', 'PASS', 'FLAG']
}
row_metadata = {
'PlateId': ['A13', 'A13'],
'Barcode': ['SL1236', 'SL1237']
}
header_metadata = {
'AdatId': '1a2b3d',
'!AssayRobot': 'Tecan2',
'RunNotes': 'run note 2'
}
mismatch_seq_id_adat = Adat.from_features(rfu_data, row_metadata,
col_metadata,
header_metadata)
with self.assertRaises(AdatMetaError):
mismatch_seq_id_adat.update_somamer_metadata_from_adat(self.adat0)
def test_col_meta_replaced(self):
rfu_data = [[5, 6, 7], [6, 5, 4]]
col_metadata = {
'SeqId': ['A', 'B', 'C'],
'SeqIdVersion': ['1', '2', '3'],
'ColCheck': ['PASS', 'PASS', 'FLAG']
}
row_metadata = {
'PlateId': ['A13', 'A13'],
'Barcode': ['SL1236', 'SL1237']
}
header_metadata = {
'AdatId': '1a2b3d',
'!AssayRobot': 'Tecan2',
'RunNotes': 'run note 2'
}
truth_meta_replaced_adat_1 = Adat.from_features(
rfu_data, row_metadata, col_metadata, header_metadata)
meta_replaced_adat = self.adat1.update_somamer_metadata_from_adat(
self.adat0)
pd.testing.assert_frame_equal(truth_meta_replaced_adat_1,
meta_replaced_adat)
def read_file(filepath: str) -> Adat:
"""Returns an Adat from the filepath/name.
Parameters
----------
filepath: str
Either the absolute or relative path to the file to be opened.
Examples
--------
>>> adat = Adat.from_file('path/to/file.adat')
Returns
-------
adat : Adat
"""
with open(filepath, 'r') as f:
rfu_matrix, row_metadata, column_metadata, header_metadata = parse_file(
f)
return Adat.from_features(rfu_matrix=rfu_matrix,
row_metadata=row_metadata,
column_metadata=column_metadata,
header_metadata=header_metadata)
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)