print 'fragments', fragments
patients = load_patients()
if pnames is not None:
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:
regions = args.regions
VERBOSE = args.verbose
save_to_file = args.save
patients = load_patients()
if pnames is not None:
patients = patients.loc[pnames]
if VERBOSE >= 3:
print 'patients', patients.index
if not len(patients):
raise ValueError('No patients found!')
maps_coord = defaultdict(dict)
for pname, patient in patients.iterrows():
patient = Patient(patient)
# Make maps for all annotations if not explicit
if regions is None:
patseqann = patient.get_reference('genomewide', format='gb')
regionspat = map(attrgetter('id'), patseqann.features) + ['genomewide']
else:
regionspat = regions
for region in regionspat:
if VERBOSE >= 1:
print pname, region
coomap = patient.get_map_coordinates_reference(region,
refname=refname)
regions = args.regions
VERBOSE = args.verbose
save_to_file = args.save
patients = load_patients()
if pnames is not None:
patients = patients.loc[pnames]
if VERBOSE >= 3:
print 'patients', patients.index
if not len(patients):
raise ValueError('No patients found!')
maps_coord = defaultdict(dict)
for pname, patient in patients.iterrows():
patient = Patient(patient)
# Make maps for all annotations if not explicit
if regions is None:
patseqann = patient.get_reference('genomewide', format='gb')
regionspat = map(attrgetter('id'),
patseqann.features) + ['genomewide']
else:
regionspat = regions
for region in regionspat:
if VERBOSE >= 1:
print pname, region
coomap = patient.get_map_coordinates_reference(region,
refname=refname)
