From 0cd6d05960697c36896ab9b71e02d18af514bb96 Mon Sep 17 00:00:00 2001
From: Auden Cote-L'Heureux <52716489+AudenCote@users.noreply.github.com>
Date: Mon, 4 Dec 2023 16:04:46 -0500
Subject: [PATCH] Temporarily removing contamination loop

---
 PTL2/Scripts/phylotol.py | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/PTL2/Scripts/phylotol.py b/PTL2/Scripts/phylotol.py
index bea7f50..e54a159 100644
--- a/PTL2/Scripts/phylotol.py
+++ b/PTL2/Scripts/phylotol.py
@@ -1,6 +1,5 @@
 #!/usr/bin/python3
 import os, sys, re
-import contamination
 import utils
 import preguidance
 import guidance
@@ -28,10 +27,6 @@ if __name__ == '__main__':
 		print('\nBuilding trees\n')
 		trees.run(params)
 
-	if params.contamination_loop != None:
-		print('\nRunning contamination loop\n')
-		contamination.run(params)
-
 	if params.concatenate:
 		print('\nChoosing orthologs and concatenating alignments...\n')
 		concatenate.run(params)