From fb6e7aa6e7bb3b7d474b33fcfc9f096e3bec212d Mon Sep 17 00:00:00 2001
From: Auden Cote-L'Heureux <52716489+AudenCote@users.noreply.github.com>
Date: Fri, 1 Nov 2024 10:34:57 -0400
Subject: [PATCH] Changing CladeGrabbing.py to use less than or equal to for
 number of contaminants

---
 Utilities/for_trees/CladeGrabbing.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Utilities/for_trees/CladeGrabbing.py b/Utilities/for_trees/CladeGrabbing.py
index e48d2ad..fe6476a 100644
--- a/Utilities/for_trees/CladeGrabbing.py
+++ b/Utilities/for_trees/CladeGrabbing.py
@@ -158,7 +158,7 @@ def get_subtrees(args, file):
 
 
 				#Grab a clade as a subtree if 1) it has enough target taxa; 2) it has enough "at least" taxa; 3) it does not have too many contaminants
-				if len(target_leaves) >= args.min_presence and len(required_taxa_leaves) >= args.required_taxa_num and ((args.contaminants < 1 and len(leaves) < args.contaminants * len(target_leaves)) or len(leaves) < args.contaminants):
+				if len(target_leaves) >= args.min_presence and len(required_taxa_leaves) >= args.required_taxa_num and ((args.contaminants < 1 and len(leaves) <= args.contaminants * len(target_leaves)) or len(leaves) <= args.contaminants):
 					selected_nodes.append(node)
 					seen_leaves.extend([leaf.name for leaf in node])
 	#Write the subtrees to output .tre files