patients = load_patients()
if pnames is not None:
patients = patients.loc[pnames]
for pname, patient in patients.iterrows():
patient = Patient(patient)
patient.discard_nonsequenced_samples()
if VERBOSE >= 1:
print patient.name, roi
if VERBOSE >= 2:
print 'Get haplotype trajectories'
try:
(ht, indt, htseqs) = patient.get_region_count_trajectories(roi[0],
VERBOSE=VERBOSE)
except IOError:
(ht, indt, htseqs) = patient.get_local_haplotype_count_trajectories(roi,
VERBOSE=VERBOSE)
if VERBOSE >= 2:
print 'Align haplotypes and delete rare ones'
indht = (ht > 5).any(axis=0)
ht = ht[:, indht]
htseqs = htseqs[indht]
# Eliminate time points that are empty after this filter
ind_keep = ht.any(axis=1)
indt = indt[ind_keep]
ht = ht[ind_keep]
patients = load_patients()
if pnames is not None:
patients = patients.loc[pnames]
data = []
for pname, patient in patients.iterrows():
patient = Patient(patient)
for region in regions:
if VERBOSE >= 1:
print patient.name, region
if VERBOSE >= 2:
print 'Get haplotype counts'
(hct, ind, seqs) = patient.get_region_count_trajectories(region,
VERBOSE=VERBOSE)
times = patient.times[ind]
if VERBOSE >= 2:
print 'Align sequences'
ali = align_muscle(*seqs, sort=True)
alim = np.array(ali)
if VERBOSE >= 2:
print 'Get distributions'
ds = get_distance_distributions(hct, alim, VERBOSE=VERBOSE)
data.append({'pname': pname, 'ds': ds, 't': times,
'region': region})
if pnames is not None:
patients = patients.loc[pnames]
for pname, patient in patients.iterrows():
patient = Patient(patient)
patient.discard_nonsequenced_samples()
if VERBOSE >= 1:
print patient.name, roi
if VERBOSE >= 2:
print 'Get haplotype trajectories'
try:
(ht, indt,
htseqs) = patient.get_region_count_trajectories(roi[0],
VERBOSE=VERBOSE)
except IOError:
(ht, indt,
htseqs) = patient.get_local_haplotype_count_trajectories(
roi, VERBOSE=VERBOSE)
if VERBOSE >= 2:
print 'Align haplotypes and delete rare ones'
indht = (ht > 5).any(axis=0)
ht = ht[:, indht]
htseqs = htseqs[indht]
# Eliminate time points that are empty after this filter
ind_keep = ht.any(axis=1)
indt = indt[ind_keep]
ht = ht[ind_keep]
