args = parser.parse_args()
pnames = args.patients
roi = args.roi
VERBOSE = args.verbose
use_plot = args.plot
use_interactive = args.interactive
patients = load_patients()
if pnames is not None:
patients = patients.loc[pnames]
for pname, patient in patients.iterrows():
patient = Patient(patient)
(fragment, start, end) = patient.get_fragmented_roi(roi, VERBOSE=VERBOSE)
aft, ind = patient.get_allele_frequency_trajectories(fragment)
aft = aft[:, :, start:end]
# TODO: also calculate the logos
## Get only some time points
# i = np.arange(len(ind))[::len(ind) // 2]
# aft = aft[i]
# ind = ind[i]
times = patient.times[ind]
if use_plot:
fig, axs = plt.subplots(aft.shape[0], 1, figsize=(14, 3 * aft.shape[0]))
args = parser.parse_args()
pnames = args.patients
roi = args.roi
VERBOSE = args.verbose
use_plot = args.plot
use_interactive = args.interactive
patients = load_patients()
if pnames is not None:
patients = patients.loc[pnames]
for pname, patient in patients.iterrows():
patient = Patient(patient)
(fragment, start, end) = patient.get_fragmented_roi(roi,
VERBOSE=VERBOSE)
aft, ind = patient.get_allele_frequency_trajectories(fragment)
aft = aft[:, :, start:end]
# TODO: also calculate the logos
## Get only some time points
#i = np.arange(len(ind))[::len(ind) // 2]
#aft = aft[i]
#ind = ind[i]
times = patient.times[ind]
if use_plot:
fig, axs = plt.subplots(aft.shape[0],
1,
