From 7348c7445fa40a57c58935bc3c537fbf31e6f366 Mon Sep 17 00:00:00 2001
From: Auden Cote-L'Heureux <52716489+AudenCote@users.noreply.github.com>
Date: Sun, 19 Jan 2025 11:04:41 -0500
Subject: [PATCH] updating header in CUB.py

---
 PTL1/Transcriptomes/Scripts/CUB.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/PTL1/Transcriptomes/Scripts/CUB.py b/PTL1/Transcriptomes/Scripts/CUB.py
index cd5aad0..215a668 100644
--- a/PTL1/Transcriptomes/Scripts/CUB.py
+++ b/PTL1/Transcriptomes/Scripts/CUB.py
@@ -3,10 +3,12 @@
 
 # The aim of this script is to generate lots of codon usage statistics to aid in
 # identifying useful characteristics for de novo ORF calling. It is intended to be
-# stored in the 'Scripts' folder for the PhyloToL Part 1 pipeline scripts, and is
+# stored in the 'Scripts' folder for the EukPhylo Part 1 pipeline scripts, and is
 # called by Script 7b to calculate composition statistics for Part 1 output files.
 # It should not be run separately.
 
+# Users should think about including start/stop constraint as default includes all 
+# sequences, which can capture pseudogenes
 
 # Dependencies:
 # Python3, numpy, BioPython