def make_basecall_input_multi(fast5_files, section='template', window=[-1, 0, 1], trim=10, min_len=1000, max_len=9000,
event_detect=True, ed_params={'window_lengths':[3, 6], 'thresholds':[1.4, 1.1], 'peak_height':0.2}, sloika_model=False):
"""Like the above, but doesn't yields directly events. The point here is to
be fully consistent with the currennt interface but allow use of the python
library
"""
for f in fast5_files:
with Fast5(f) as fh:
if event_detect:
# These parameters make no sense to me, but hey-ho
# TODO: expose to user
events = minknow_event_detect(
fh.get_read(raw=True), fh.sample_rate, **ed_params
)
else:
events = fh.get_read()
events, _ = segment(events, section=section)
try:
X = events_to_features(events, window=window, sloika_model=sloika_model)
except TypeError:
continue
try:
X = X[trim:-trim]
events = events[trim:-trim]
except:
continue
else:
if len(X) < min_len or len(X) > max_len:
continue
yield f, X, events
def basecall_file(fname=None, event_detect=True):
"""Read event data from file and print scrappie basecall.
:param fname: filename to read data from (if not given assumed
to be given on command line.
:param event_detect: do event detection?
:returns: tuple (basecall score, sequence).
"""
is_main = False
if fname is None: #called as entrypoint
fname = sys.argv[1]
is_main = True
# magic numbers
ed_params = {
'window_lengths':[4, 8],
'thresholds': [1.5, 9.0],
'peak_height': 0.2,
}
with Fast5(fname) as fh:
if event_detect:
events = minknow_event_detect(
fh.get_read(raw=True), fh.sample_rate, **ed_params
)
else:
events = fh.get_read()
events, _ = segment(events, section='template')
results = basecall_events(events)
if results is None:
return None
if is_main:
print("{} score={}\n{}".format(fname, *results))
else:
return results
def basecall_file(fname=None, event_detect=True):
"""Read event data from file and print scrappie basecall.
:param fname: filename to read data from (if not given assumed
to be given on command line.
:param event_detect: do event detection?
:returns: tuple (basecall score, sequence).
"""
is_main = False
if fname is None: #called as entrypoint
fname = sys.argv[1]
is_main = True
# magic numbers
ed_params = {
'window_lengths': [4, 8],
'thresholds': [1.5, 9.0],
'peak_height': 0.2,
}
with Fast5(fname) as fh:
if event_detect:
events = minknow_event_detect(fh.get_read(raw=True),
fh.sample_rate, **ed_params)
else:
events = fh.get_read()
events, _ = segment(events, section='template')
results = basecall_events(events)
if results is None:
return None
if is_main:
print("{} score={}\n{}".format(fname, *results))
else:
return results