From b07b29af612cbc99d32e49b287b7b9a6965fa1f6 Mon Sep 17 00:00:00 2001 From: Nikolai Romashchenko Date: Sun, 20 Oct 2024 22:42:04 +0200 Subject: [PATCH] Added -m pvalue --- omamer/main.py | 2 +- omamer/merge_search.py | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/omamer/main.py b/omamer/main.py index ea343db..6b8e6ae 100644 --- a/omamer/main.py +++ b/omamer/main.py @@ -248,7 +248,7 @@ def get_thread_count(): "-m", "--method", default="normcount", - choices=["normcount", "zscore", "rawcount"], + choices=["normcount", "zscore", "rawcount", "pvalue"], help="Scoring scheme used to select family.", ) search_parser.add_argument( diff --git a/omamer/merge_search.py b/omamer/merge_search.py index 52c352f..8c39271 100644 --- a/omamer/merge_search.py +++ b/omamer/merge_search.py @@ -973,6 +973,8 @@ def func( ) elif method == "rawcount": qres["normcount"][:] = qres["count"] + elif method == "pvalue": + qres["normcount"][:] = qres["pvalue"] else: return