More robust default thresholds

SegataLab · Nov 3, 2021 · a7846e4 · a7846e4
1 parent 45f0244
commit a7846e4
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/panphlan_profiling.py b/panphlan_profiling.py
@@ -58,11 +58,11 @@ def read_params():
     p.add_argument('--right_min', type=float, default=0.75, # v1.0: 0.82
                    help='Strain presence/absence plateau curve threshold: right min [0.75]')
     # Gene families presence/absence threshold
-    p.add_argument('--th_non_present', type=float, default = 0.05,
+    p.add_argument('--th_non_present', type=float, default = 0.25,
                    help='Gene families threshold: not present if lower')
-    p.add_argument('--th_present', type=float, default = 0.1,
+    p.add_argument('--th_present', type=float, default = 0.5,
                    help='Gene families threshold: present if higher')
-    p.add_argument('--th_multicopy', type=float, default = 0.15,
+    p.add_argument('--th_multicopy', type=float, default = 1.5,
                    help='Gene families threshold: multicopy if higher')
     # filter similarity
     p.add_argument('--strain_similarity_perc', metavar='SIMILARITY_PERCENTAGE', type=float, default=50.0,