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 plot:
plot_divdiv_trajectory(patient, VERBOSE=VERBOSE)
if plot:
plt.ion()
plt.show()
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 plot:
plot_divdiv_trajectory(patient, VERBOSE=VERBOSE)
if plot:
plt.ion()
plt.show()
patients = patients.iloc[patients.index.isin(pnames)]
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 fragment in fragments:
if VERBOSE >= 1:
print pname, fragment
covt, ind = patient.get_coverage_trajectories(fragment,
use_PCR1=use_PCR1)
samples = patient.samples.iloc[ind]
times = patient.times[ind]
ntemplates = samples['n templates']
if plot is not None:
import matplotlib.pyplot as plt
if plot in ('2D', '2d', ''):
labels = [
str(t) + ': ' + s
for (t, s) in izip(times, samples.index)
]
legtitle = 'Time from transmission [days]: sample name'
plot_coverage_trajectories(times,
covt,
patients = patients.iloc[patients.index.isin(pnames)]
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 fragment in fragments:
if VERBOSE >= 1:
print pname, fragment
covt, ind = patient.get_coverage_trajectories(fragment,
use_PCR1=use_PCR1)
samples = patient.samples.iloc[ind]
times = patient.times[ind]
ntemplates = samples['n templates']
if plot is not None:
import matplotlib.pyplot as plt
if plot in ('2D', '2d', ''):
labels = [str(t)+': '+s for (t, s) in izip(times, samples.index)]
legtitle = 'Time from transmission [days]: sample name'
plot_coverage_trajectories(times, covt,
title='Patient '+pname+', '+fragment,
labels=labels,
legendtitle=legtitle,
VERBOSE=VERBOSE)
