if not fragments:
fragments = ['F' + str(i) for i in xrange(1, 7)]
if VERBOSE >= 2:
print 'fragments', fragments
for pname, patient in patients.iterrows():
patient = Patient(patient)
patient.discard_nonsequenced_samples()
for ifr, fragment in enumerate(fragments):
if VERBOSE >= 1:
print pname, fragment
dg, ind, block_length, L = \
patient.get_divergence_trajectory_local(fragment,
block_length=block_length)
ds, ind, block_length, L = \
patient.get_diversity_trajectory_local(fragment,
block_length=block_length)
patient.dg = dg
patient.ds = ds
patient.ind = ind
patient.L = L
patient.block_length = block_length
if use_coverage:
(covt, ind2) = patient.get_coverage_trajectories(fragment)
if set(ind).symmetric_difference(set(ind2)):
raise ValueError(
'Indices for allele freqs and coverage differ!')
patient.covt = covt
if not fragments:
fragments = ['F'+str(i) for i in xrange(1, 7)]
if VERBOSE >= 2:
print 'fragments', fragments
for pname, patient in patients.iterrows():
patient = Patient(patient)
patient.discard_nonsequenced_samples()
for ifr, fragment in enumerate(fragments):
if VERBOSE >= 1:
print pname, fragment
dg, ind, block_length, L = \
patient.get_divergence_trajectory_local(fragment,
block_length=block_length)
ds, ind, block_length, L = \
patient.get_diversity_trajectory_local(fragment,
block_length=block_length)
patient.dg = dg
patient.ds = ds
patient.ind = ind
patient.L = L
patient.block_length = block_length
if use_coverage:
(covt, ind2) = patient.get_coverage_trajectories(fragment)
if set(ind).symmetric_difference(set(ind2)):
raise ValueError('Indices for allele freqs and coverage differ!')
patient.covt = covt
