def main():
parser = argparse.ArgumentParser(
description='LOL HI THERE',
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('--use-supervars', action='store_true')
# This takes Pairtree rather than PWGS inputs, which seems a little weird,
# but it's okay -- the PWGS inputs are the supervariants, but we need to know
# which variants correspond to each cluster in the original Pairtree inputs.
parser.add_argument('tree_summary', help='JSON-formatted tree summaries')
parser.add_argument('mutation_list',
help='JSON-formatted list of mutations')
parser.add_argument(
'mutation_assignment',
help='JSON-formatted list of SSMs and CNVs assigned to each subclone')
parser.add_argument('pairtree_params_fn')
parser.add_argument('neutree_fn')
args = parser.parse_args()
results = ResultLoader(args.tree_summary, args.mutation_list,
args.mutation_assignment)
if args.use_supervars:
params = inputparser.load_params(args.pairtree_params_fn)
base_clusters = params['clusters']
garbage = params['garbage']
else:
base_clusters = None
garbage = []
ntree = convert_results(results, base_clusters, garbage,
args.use_supervars)
neutree.save(ntree, args.neutree_fn)
def main():
parser = argparse.ArgumentParser(
description='LOL HI THERE',
formatter_class=argparse.ArgumentDefaultsHelpFormatter
)
parser.add_argument('pairtree_results_fn')
parser.add_argument('params_fn')
parser.add_argument('neutree_fn')
args = parser.parse_args()
results = resultserializer.Results(args.pairtree_results_fn)
params = inputparser.load_params(args.params_fn)
ntree = convert(results, params['garbage'])
neutree.save(ntree, args.neutree_fn)
def write_neutree(results, garbage, neutree_fn):
adjms = [R['adjm'] for R in results]
structs = [util.convert_adjmatrix_to_parents(A) for A in adjms]
llhs = [R['llh'] for R in results]
clusterings = [R['clusters'] for R in results]
phis = [R['phi'] for R in results]
N = len(structs)
counts = np.ones(N)
ntree = neutree.Neutree(
structs=structs,
phis=phis,
counts=counts,
logscores=llhs,
clusterings=clusterings,
garbage=garbage,
)
neutree.save(ntree, neutree_fn)
def convert(sampid, params_fn, trees_fn, neutree_fn):
adjms, llhs, phis, clusterings = pastri_util.load_results(
sampid, params_fn, trees_fn)
if len(adjms) == 0:
return
structs = [util.convert_adjmatrix_to_parents(A) for A in adjms]
N = len(structs)
params = inputparser.load_params(params_fn)
ntree = neutree.Neutree(
structs=structs,
phis=phis,
counts=np.ones(N),
logscores=llhs,
clusterings=clusterings,
garbage=params['garbage'],
)
neutree.save(ntree, neutree_fn)
def convert(params_fn, calder_mats_fn, calder_trees_fn, neutree_fn):
params = inputparser.load_params(params_fn)
mats, row_labels, col_labels = _load_mats(calder_mats_fn)
assert row_labels['Fhat'][0] == 'samples'
svids = row_labels['Fhat'][1:]
assert svids == common.sort_vids(svids)
struct = _load_struct(svids, calder_trees_fn)
ntree = neutree.Neutree(
structs=[struct],
phis=[mats['Fhat']],
counts=np.array([1]),
logscores=np.array([0.]),
clusterings=[params['clusters']],
garbage=params['garbage'],
)
neutree.save(ntree, neutree_fn)