diff --git a/prob2020/python/p_value.py b/prob2020/python/p_value.py index ec17003..666a73f 100644 --- a/prob2020/python/p_value.py +++ b/prob2020/python/p_value.py @@ -127,24 +127,14 @@ def calc_deleterious_p_value(mut_info, # least meet some user-specified threshold if num_del >= del_threshold: # perform permutations - #if len(mut_info) > 0: del_p_value = pm.deleterious_permutation(num_del, - context_cts, - context_to_mutations, - sc, # sequence context obj - gs, # gene sequence obj - num_permutations, - stop_thresh, - pseudo_count) - #else: - # no SNV mutation case - #null_del_list = [0 for i in range(num_permutations)] - #del_p_value = 1.0 - - # calculate p-value - #del_num_nulls = sum([1 for d in null_del_list - #if d+utils.epsilon >= num_del]) - #del_p_value = del_num_nulls / float(num_permutations) + context_cts, + context_to_mutations, + sc, # sequence context obj + gs, # gene sequence obj + num_permutations, + stop_thresh, + pseudo_count) else: del_p_value = None else: