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PTL1/Genomes/Scripts/CUB.py
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# Last updated Sept 2023
# Author: Xyrus Maurer-Alcalá
# Author: Xyrus Maurer-Alcalá and Auden Cote-L'Heureux
# 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 5b 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