def test_011_v0_6_raw(self):
# Check that it is recognized properly.
fname = os.path.join(test_data, 'read_file_v0.6_raw.fast5')
result = Fast5Info(fname)
self.assertEqual(0.6, result.version)
# Copy file and Update to current format.
new_file = self.generate_temp_filename()
copyfile(fname, new_file)
Fast5File.update_legacy_file(new_file)
result = Fast5Info(new_file)
self.assertEqual(CURRENT_FAST5_VERSION, result.version)
self.assertEqual(1, len(result.read_info))
self.assertEqual(627, result.read_info[0].read_number)
# Load the event data.
with Fast5File(new_file, mode='r') as fh:
analist = fh.list_analyses('event_detection')
self.assertEqual(1, len(analist))
group = '{}/Reads/Read_627'.format(analist[0][1])
data = fh.get_analysis_dataset(group, 'Events')
self.assertEqual(2337, data.size)
self.assertEqual(set(('mean', 'stdv', 'start', 'length')),
set(data.dtype.names))
read_info = fh.status.read_info[0]
self.assertEqual(2337, read_info.event_data_count)
channel_info = fh.get_channel_info()
self.assertEqual(118, channel_info['channel_number'])
raw = fh.get_raw_data(read_number=627)
self.assertEqual(46037, raw.size)
self.assertEqual(46037, read_info.duration)
def test_012_v1_0_single(self):
# Check that it is recognized properly.
fname = os.path.join(test_data, 'read_file_v1.0_single.fast5')
result = Fast5Info(fname)
self.assertEqual(1.0, result.version)
# Copy file and Update to current format.
new_file = os.path.join(self.save_path, 'single_read_v1.0_test.fast5')
copyfile(fname, new_file)
Fast5File.update_legacy_file(new_file)
result = Fast5Info(new_file)
self.assertEqual(1.1, result.version)
self.assertEqual(1, len(result.read_info))
self.assertEqual(59, result.read_info[0].read_number)
# Load the event data.
with Fast5File(new_file, mode='r') as fh:
analist = fh.list_analyses('event_detection')
self.assertEqual(1, len(analist))
group = '{}/Reads/Read_59'.format(analist[0][1])
data = fh.get_analysis_dataset(group, 'Events')
self.assertEqual(7875, data.size)
self.assertEqual(set(('mean', 'stdv', 'start', 'length')),
set(data.dtype.names))
read_info = fh.status.read_info[0]
self.assertEqual(7875, read_info.event_data_count)
channel_info = fh.get_channel_info()
self.assertEqual(1, channel_info['channel_number'])
def __init__(self, fname, mode='r'):
""" Constructor. Opens the specified file.
:param fname: Filename to open.
:param mode: File open mode (r, r+, w, w-, x).
"""
if mode not in ['r', 'r+', 'w', 'w-', 'x']:
raise IOError('Unsupported file handle mode : "{}" use {}'.format(
mode, ['r', 'r+', 'w', 'w-', 'x']))
self.filename = fname
self.handle = None
self._is_open = False
if mode in ['w', 'w-', 'x']:
with h5py.File(fname, mode) as fh:
fh.attrs['file_version'] = CURRENT_FAST5_VERSION
fh.create_group('Analyses')
fh.create_group('Raw/Reads')
fh.create_group('UniqueGlobalKey/channel_id')
fh.create_group('UniqueGlobalKey/context_tags')
fh.create_group('UniqueGlobalKey/tracking_id')
mode = 'r+'
self.mode = mode
self.status = Fast5Info(self.filename)
if self.status.valid:
self.handle = h5py.File(self.filename, self.mode)
self._is_open = True
def _initialise_file(self):
if self.mode in ['w', 'w-', 'x']:
with h5py.File(self.filename, self.mode) as fh:
fh.attrs['file_version'] = CURRENT_FAST5_VERSION
fh.create_group('Analyses')
fh.create_group('Raw/Reads')
fh.create_group(self.global_key + 'channel_id')
fh.create_group(self.global_key + 'context_tags')
fh.create_group(self.global_key + 'tracking_id')
self.mode = 'r+'
self.status = Fast5Info(self.filename)
if self.status.valid:
self.handle = h5py.File(self.filename, self.mode)
self._is_open = True
def __init__(self, filename):
""" Constructor. Opens the specified file
:param filename: Filename to open
"""
# Attributes Initializeation
self.filename = filename
self.handle = None
self._is_open = False
self.status = Fast5Info(self.filename)
self.events = None
if self.status.valid:
self.handle = h5py.File(self.filename,
'r') # Open the file in read-only mode
self._is_open = True
def _initialise_file(self):
try:
if self.mode in ['w', 'w-', 'x']:
with h5py.File(self.filename, self.mode) as fh:
fh.attrs['file_version'] = CURRENT_FAST5_VERSION
fh.create_group('Analyses')
fh.create_group('Raw/Reads')
fh.create_group(self.global_key + 'channel_id')
fh.create_group(self.global_key + 'context_tags')
fh.create_group(self.global_key + 'tracking_id')
self.mode = 'r+'
self.status = Fast5Info(self.filename)
if self.status.valid:
self.handle = h5py.File(self.filename, self.mode)
except Exception:
raise Fast5FileTypeError(
"Failed to initialise single-read Fast5File: '{}'".format(
self.filename))
def _initialise_file(self):
if self.mode == 'r': # For read-only files, copy the file to (hopefully) faster storage
from tempfile import NamedTemporaryFile
from shutil import copyfile
self._readonly_file_obj = NamedTemporaryFile()
copyfile(self.filename, self._readonly_file_obj.name)
self.filename = self._readonly_file_obj.name
elif self.mode in ['w', 'w-', 'x']:
with h5py.File(self.filename, self.mode) as fh:
fh.attrs['file_version'] = CURRENT_FAST5_VERSION
fh.create_group('Analyses')
fh.create_group('Raw/Reads')
fh.create_group(self.global_key + 'channel_id')
fh.create_group(self.global_key + 'context_tags')
fh.create_group(self.global_key + 'tracking_id')
self.mode = 'r+'
self.status = Fast5Info(self.filename)
if self.status.valid:
self.handle = h5py.File(self.filename, self.mode)
self._is_open = True
def update_legacy_file(fname):
""" Update a fast5 file from an older version to the new standard.
:param fname: The filename of the fast5 file.
"""
status = Fast5Info(fname)
if not status.valid:
raise IOError('Cannot update invalid file: {}'.format(fname))
with h5py.File(fname, 'r+') as handle:
# Add Raw/Read/Read_## groups for reads if they are missing.
for read_info in status.read_info:
read_group_name = 'Raw/Reads/Read_{}'.format(
read_info.read_number)
if read_group_name in handle:
rgh = handle[read_group_name]
else:
rgh = handle.create_group(read_group_name)
rgh.attrs['read_number'] = read_info.read_number
rgh.attrs['read_id'] = read_info.read_id
rgh.attrs['duration'] = read_info.duration
rgh.attrs['start_time'] = read_info.start_time
rgh.attrs['start_mux'] = read_info.start_mux
# Add the Analyses and tracking_id groups, if they are missing.
if not 'Analyses' in handle:
handle.create_group('Analyses')
if not 'tracking_id' in handle['UniqueGlobalKey']:
handle.create_group('UniqueGlobalKey/tracking_id')
# Update the EventDetection_000 created by old versions of MinKNOW, if needed.
if status.version < 1.1:
if 'Analyses/EventDetection_000' in handle:
reads_group = handle['Analyses/EventDetection_000/Reads']
data_group_names = reads_group.keys()
for data_group_name in data_group_names:
read_group = reads_group[data_group_name]
read_number = read_group.attrs['read_number']
read_info = status.read_info[
status.read_number_map[read_number]]
read_group.attrs['read_id'] = read_info.read_id
if 'Events' in read_group:
dataset = read_group['Events']
if 'variance' in dataset.dtype.names:
old_data = read_group['Events'][()]
new_data = np.empty(old_data.size,
dtype=[('mean', float),
('stdv', float),
('start', int),
('length', int)])
new_data[:]['mean'] = old_data['mean']
new_data[:]['stdv'] = np.sqrt(
old_data['variance'])
new_data[:]['start'] = old_data['start']
new_data[:]['length'] = old_data['length']
del read_group['Events']
read_group.create_dataset('Events',
data=new_data,
compression='gzip')
# Update the version number.
handle.attrs['file_version'] = CURRENT_FAST5_VERSION