a.cleanup_tree()
if VERBOSE >= 2:
print 'Annotate tree'
annotate_tree_time_freq_count(tree, ali)
annotate_tree(patient, tree, VERBOSE=VERBOSE)
if VERBOSE >= 2:
print 'Ladderize tree'
tree.ladderize()
if use_save:
if VERBOSE >= 2:
print 'Save tree (JSON)'
rname = 'scan_'+str(win_start)+'-'+str(win_end)
fn = patient.get_local_tree_filename(rname, format='json')
mkdirs(os.path.dirname(fn))
tree_json = tree_to_json(tree.root,
fields=('DSI', 'sequence',
'muts',
'VL', 'CD4',
'frequency',
'count',
'confidence'),
)
write_json(tree_json, fn)
if use_plot:
if VERBOSE >= 2:
print 'Plot'
plot_tree(tree, title=patient.code+', '+str(win_start)+'-'+str(win_end))
maxreads = args.maxreads
use_plot = args.plot
freqmin = args.freqmin
patients = load_patients()
if pnames is not None:
patients = patients.loc[pnames]
for pname, patient in patients.iterrows():
patient = Patient(patient)
if VERBOSE >= 1:
print pname
if os.path.isfile(
patient.get_local_tree_filename(roi[0], format='json')):
if VERBOSE >= 2:
print 'Get tree'
region = roi[0]
tree = patient.get_local_tree(region)
elif os.path.isfile(
patient.get_local_tree_filename(' '.join(map(str, roi)),
format='json')):
if VERBOSE >= 2:
print 'Get tree'
region = ' '.join(map(str, roi))
tree = patient.get_local_tree(region)
else:
raise IOError('Tree file not found')
a.cleanup_tree()
if VERBOSE >= 2:
print 'Annotate tree'
annotate_tree_time_freq_count(tree, ali)
annotate_tree(patient, tree, VERBOSE=VERBOSE)
if VERBOSE >= 2:
print 'Ladderize tree'
tree.ladderize()
if use_save:
if VERBOSE >= 2:
print 'Save tree (JSON)'
rname = 'scan_' + str(win_start) + '-' + str(win_end)
fn = patient.get_local_tree_filename(rname, format='json')
mkdirs(os.path.dirname(fn))
tree_json = tree_to_json(
tree.root,
fields=('DSI', 'sequence', 'muts', 'VL', 'CD4',
'frequency', 'count', 'confidence'),
)
write_json(tree_json, fn)
if use_plot:
if VERBOSE >= 2:
print 'Plot'
plot_tree(tree,
title=patient.code + ', ' + str(win_start) + '-' +
str(win_end))
VERBOSE = args.verbose
maxreads = args.maxreads
use_plot = args.plot
freqmin = args.freqmin
patients = load_patients()
if pnames is not None:
patients = patients.loc[pnames]
for pname, patient in patients.iterrows():
patient = Patient(patient)
if VERBOSE >= 1:
print pname
if os.path.isfile(patient.get_local_tree_filename(roi[0], format='json')):
if VERBOSE >= 2:
print 'Get tree'
region = roi[0]
tree = patient.get_local_tree(region)
elif os.path.isfile(patient.get_local_tree_filename(' '.join(map(str, roi)), format='json')):
if VERBOSE >= 2:
print 'Get tree'
region = ' '.join(map(str, roi))
tree = patient.get_local_tree(region)
else:
raise IOError('Tree file not found')
if VERBOSE >= 2:
