def test_old_version(self):
records = read_records(self.sample_stream, min_version=3)
self.assertRaisesRegexp(
IOError,
'File version 1 is less than minimum version 3 in test_file.',
records.next)
def test_old_version(self):
records = read_records(self.sample_stream, min_version=3)
self.assertRaisesRegex(
IOError,
'File version 1 is less than minimum version 3 in test_file.',
records.__next__)
def test_load_multiple_records(self):
self.sample_data[1] = 2 # record size
self.pack_data()
expected_records = ['AB', 'CD']
records = list(read_records(self.sample_stream, min_version=1))
self.assertEqual(expected_records, records)
def test_load_multiple_records(self):
self.sample_data[1] = 2 # record size
self.pack_data()
expected_records = [b'AB', b'CD']
records = list(read_records(self.sample_stream, min_version=1))
self.assertEqual(expected_records, records)
def test_partial_record(self):
self.sample_data[1] = 3
self.pack_data()
records = read_records(self.sample_stream, min_version=1)
record1 = records.next()
self.assertEqual('ABC', record1)
self.assertRaisesRegexp(
IOError, 'Partial record of length 1 found in test_file.',
records.next)
def test_partial_record(self):
self.sample_data[1] = 3
self.pack_data()
records = read_records(self.sample_stream, min_version=1)
record1 = next(records)
self.assertEqual(b'ABC', record1)
self.assertRaisesRegex(
IOError,
'Partial record of length 1 found in test_file.',
records.__next__)
def read_tiles(data_file):
""" Read a tile metrics data file.
:param file data_file: an open file-like object. Needs to have a two-byte
header with the file version and the length of each record, followed by the
records.
:return: an iterator over the records of data in the file. Each record is a
dictionary with the following keys:
- lane [uint16]
- tile [uint16]
- metric_code [uint16]
- metric_value [float32]
"""
PARSED_LENGTH = 10
format_string = '<HHHf'
for data in read_records(data_file, min_version=2):
fields = unpack(format_string, data[:PARSED_LENGTH])
yield dict(lane=fields[0],
tile=fields[1],
metric_code=fields[2],
metric_value=fields[3])
def read_quality(data_file):
""" Read a quality metrics data file.
:param file data_file: an open file-like object. Needs to have a two-byte
header with the file version and the length of each record, followed by the
records.
:return: an iterator over the records of data in the file. Each record is a
dictionary with the following keys:
- lane [uint16]
- tile [uint16]
- cycle [uint16]
- quality_bins [list of 50 uint32, representing quality 1 to 50]
"""
PARSED_LENGTH = 206
format_string = '<HHH' + 'L' * 50
for data in read_records(data_file, min_version=4):
fields = unpack(format_string, data[:PARSED_LENGTH])
yield dict(lane=fields[0],
tile=fields[1],
cycle=fields[2],
quality_bins=fields[3:])
def read_quality(data_file):
""" Read a quality metrics data file.
:param file data_file: an open file-like object. Needs to have a two-byte
header with the file version and the length of each record, followed by the
records.
:return: an iterator over the records of data in the file. Each record is a
dictionary with the following keys:
- lane [uint16]
- tile [uint16]
- cycle [uint16]
- quality_bins [list of 50 uint32, representing quality 1 to 50]
"""
PARSED_LENGTH = 206
format_string = '<HHH' + 'L'*50
for data in read_records(data_file, min_version=4):
fields = unpack(format_string, data[:PARSED_LENGTH])
yield dict(lane=fields[0],
tile=fields[1],
cycle=fields[2],
quality_bins=fields[3:])
def read_tiles(data_file):
""" Read a tile metrics data file.
:param file data_file: an open file-like object. Needs to have a two-byte
header with the file version and the length of each record, followed by the
records.
:return: an iterator over the records of data in the file. Each record is a
dictionary with the following keys:
- lane [uint16]
- tile [uint16]
- metric_code [uint16]
- metric_value [float32]
"""
PARSED_LENGTH = 10
format_string = '<HHHf'
for data in read_records(data_file, min_version=2):
fields = unpack(format_string, data[:PARSED_LENGTH])
yield dict(lane=fields[0],
tile=fields[1],
metric_code=fields[2],
metric_value=fields[3])
def test_load(self):
expected_records = ['ABCD']
records = list(read_records(self.sample_stream, min_version=1))
self.assertEqual(expected_records, records)
def test_load(self):
expected_records = [b'ABCD']
records = list(read_records(self.sample_stream, min_version=1))
self.assertEqual(expected_records, records)
