VERBOSE = args.verbose
use_plot = args.plot
patients = load_patients()
if pnames:
patients = patients.loc[pnames]
for pname, patient in patients.iterrows():
patient = Patient(patient)
patient.discard_nonsequenced_samples()
for region in regions:
if VERBOSE >= 1:
print pname, region
ali = patient.get_consensi_alignment(region)
tree = patient.get_consensi_tree(region, format='json')
if use_plot:
fig, ax = plt.subplots(figsize=(15, 12))
Phylo.draw(tree, do_show=False, axes=ax)
ax.set_title(pname+', '+region)
x_max = max(tree.depths().itervalues())
ax.set_xlim(0.998, 0.998 + (x_max - 0.998) * 1.5)
ax.grid(True)
if use_plot:
plt.ion()
plt.show()
help='Verbosity level [0-4]')
args = parser.parse_args()
pnames = args.patients
regions = args.regions
VERBOSE = args.verbose
patients = load_patients()
if pnames:
patients = patients.loc[pnames]
alis = {}
for pname, patient in patients.iterrows():
patient = Patient(patient)
patient.discard_nonsequenced_samples()
# Guess regions if not specified
if regions is None:
refseq_gw = patient.get_reference('genomewide', 'gb')
regionspat = map(attrgetter('id'), refseq_gw.features) + ['genomewide']
else:
regionspat = regions
for region in regionspat:
if VERBOSE >= 1:
print pname, region
ali = patient.get_consensi_alignment(region)
alis[(region, pname)] = ali
