patients = patients.loc[pnames]
if VERBOSE >= 1:
print 'Analyze patients'
for pname, patient in patients.iterrows():
patient = Patient(patient)
for fragment in fragments:
if VERBOSE >= 1:
print patient.name, fragment
mapco = patient.get_map_coordinates_reference(fragment, refname=refname)
if VERBOSE >= 2:
print 'Get initial allele frequencies'
af0 = patient.get_initial_allele_frequencies(fragment, cov_min=depth_min)
if VERBOSE >= 2:
print 'Get allele frequencies'
aft, ind = patient.get_allele_frequency_trajectories(fragment,
depth_min=depth_min)
if VERBOSE >= 2:
print 'Filter out masked positions'
ind_nonmasked = -aft.mask.any(axis=0).any(axis=0)
if VERBOSE >= 2:
print 'Remove first time sample'
aft_der = aft[int(0 in ind):].copy()
if VERBOSE >= 2:
del fragments[fragments.index('genomewide')]
else:
do_genomewide = False
for pname, patient in patients.iterrows():
print pname
patient = Patient(patient)
patient.discard_nonsequenced_samples()
for fragment in fragments:
if VERBOSE >= 1:
print fragment
ref = patient.get_reference(fragment)
refm = np.array(ref, 'S1')
af0 = patient.get_initial_allele_frequencies(fragment)
consm = alpha[af0.argmax(axis=0)]
seqm = consm.copy()
# Gaps in a reference are not wished for
if '-' in seqm:
seqm[seqm == '-'] = refm[seqm == '-']
seq = SeqRecord(Seq(''.join(seqm), ambiguous_dna),
id=ref.id,
name=ref.name,
description=ref.description)
if VERBOSE >= 2:
ind = (refm != seqm).nonzero()[0]
if not len(ind):
