def create_read(self, read_id, run_id):
group_name = "read_" + read_id
if group_name not in self.handle:
try:
self.handle.create_group(group_name)
except ValueError as e:
raise_from(ValueError("Could not create group '{}' in file: {}"
.format(group_name, self.filename)), e)
self.handle[group_name].attrs["run_id"] = run_id
else:
raise ValueError("Read '{}' already exists in: {}".format(group_name, self.filename))
return Fast5Read(self, read_id)
def create_empty_read(self, read_id, run_id):
group_name = "read_" + read_id
if group_name not in self.handle:
try:
self.handle.create_group(group_name)
except ValueError as e:
raise ValueError("Could not create group '{}' in file: {}".format(group_name, self.filename)) from e
try:
for shared_group in HARDLINK_GROUPS:
self.handle["{}/{}".format(group_name, shared_group)] = \
self.handle["read_{}/{}".format(self.run_id_map[run_id], shared_group)]
except KeyError:
# If we can't hardlink to existing groups then continue as normal
# registering this read as the new source of metadata for this run_id_map
self.run_id_map[run_id] = read_id
self.handle[group_name].attrs["run_id"] = run_id
else:
raise ValueError("Read '{}' already exists in: {}".format(group_name, self.filename))
return Fast5Read(self, read_id)
def get_read(self, read_id):
group_name = "read_" + read_id
if group_name not in self.handle:
raise KeyError("Read '{}' not in: {}".format(group_name, self.filename))
return Fast5Read(self, read_id)
def get_reads(self):
for group_name in self.handle:
if group_name.startswith('read_'):
yield Fast5Read(self, group_name[5:])