def add_read(self, read_number, read_id, start_time, duration, mux,
median_before):
""" Add a new read to the file.
:param read_number: The read number to assign to the read.
:param read_id: The unique read-id for the read.
:param start_time: The start time (in samples) of the read.
:param duration: The duration (in samples) of the read.
:param mux: The mux set at the time of the read.
:param median_before: The median level of the data before the read.
Note that most tools assume a file contains only one read.
Putting multiple reads into a file severely limits the
ability to operate on those reads with standard tools.
"""
self.assert_writeable()
read_info = ReadInfo(read_number, read_id, start_time, duration, mux,
median_before)
self.status.read_info.append(read_info)
n = len(self.status.read_info) - 1
self.status.read_number_map[read_number] = n
self.status.read_id_map[read_id] = n
group_name = 'Raw/Reads/Read_{}'.format(read_number)
attrs = {
'read_number': read_number,
'read_id': read_id,
'start_time': start_time,
'duration': duration,
'start_mux': mux,
'median_before': median_before
}
self._add_group(group_name, attrs)
def test_write_vbz_using_api_single_read(self):
input_data = list(range(5))
read_id = "0a1b2c3d"
read_number = 0
with Fast5File(self.generate_temp_filename(), 'w') as fast5:
fast5.status.read_number_map[read_number] = read_number
fast5.status.read_info = [
ReadInfo(read_number=read_number,
read_id=read_id,
start_time=0,
duration=len(input_data))
]
fast5.add_raw_data(data=input_data, attrs={}, compression=VBZ)
raw = fast5.get_raw_data()
# First check the data comes back in an appropriate form
self.assertEqual(input_data, list(raw))
# Then check the types are as they should be under the hood
filters = fast5.raw_compression_filters
self.assertTrue(str(VBZ.compression) in filters)
self.assertEqual(VBZ.compression_opts,
filters[str(VBZ.compression)])