Added -m pvalue

DessimozLab · Oct 20, 2024 · b07b29a · b07b29a
1 parent f3d3b62
commit b07b29a
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diff --git 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
@@ -973,6 +973,8 @@ def func(
                     )
                 elif method == "rawcount":
                     qres["normcount"][:] = qres["count"]
+                elif method == "pvalue":
+                    qres["normcount"][:] = qres["pvalue"]
                 else:
                     return