def main():
focus_cxb, query_cxb, focus_mat, query_mat, markers, outfile, same_algorithm, same_data = parse_args(
)
query_id = "%s--%s" % (focus_mat, query_mat)
focus_cxb = io.read_cell_x_branch(focus_cxb)
query_cxb = io.read_cell_x_branch(query_cxb)
focus_mat = io.read_feature_matrix(focus_mat)
query_mat = io.read_feature_matrix(query_mat)
markers = io.read_markers(markers)
distance = dist.trajectory(focus_mat, query_mat, focus_cxb, query_cxb,
markers)
n_genes_in_calc = []
n_genes_in_markers = []
for branch in markers.keys():
n_genes_in_calc += [
len(set(markers[branch]).intersection(query_mat.columns))
]
n_genes_in_markers += [len(markers[branch])]
import numpy as np
with open(outfile, "a") as fout:
fout.write(
"%f\t%f\t%f\t%d\t%s\t%s\t%s\n" %
(distance, np.min(n_genes_in_markers), np.min(n_genes_in_calc),
len(markers.keys()), same_algorithm, same_data, query_id))
def test_trajectory_different_gt_zero():
answer = trajectory(focus, query, focus_cxb, query_cxb, f_markers_dict)
assert answer > 0
def test_trajectory_self_is_zero():
answer = trajectory(focus, focus, focus_cxb, focus_cxb, f_markers_dict)
assert answer == 0
def test_trajectory_different_markers_different():
t1 = trajectory(query, focus, query_cxb, focus_cxb, q_markers_dict)
t2 = trajectory(focus, query, focus_cxb, query_cxb, f_markers_dict)
assert t1 != t2
def test_trajectory_symmetry():
"""Test for symmetry. Must have same markers.
"""
t1 = trajectory(query, focus, query_cxb, focus_cxb, q_markers_dict)
t2 = trajectory(focus, query, focus_cxb, query_cxb, q_markers_dict)
assert t1 == t2