diff --git a/PTL1/Genomes/Scripts/2_GCodeEval.py b/PTL1/Genomes/Scripts/2_GCodeEval.py index d580c49..4875a80 100644 --- a/PTL1/Genomes/Scripts/2_GCodeEval.py +++ b/PTL1/Genomes/Scripts/2_GCodeEval.py @@ -1,18 +1,15 @@ -#!/usr/bin/env python3.5 - -##__Updated__: 19_09_2017 -##__Author__: Xyrus Maurer-Alcala; maurerax@gmail.com -##__Usage__: python 2g_GCodeEval.py --help - - -############################################################################################# -# # -# Suggests which Genetic Code to use based upon Presence/Absence of Specific Stop Codons # -# at the end of the CDS sequences. This is to provide a ROUGH gauge for the user. # -# # -############################################################################################# +# Last updated Sept 2017 +# Author: Xyrus Maurer-Alcala +# This script is intended to aid in determining which genetic code to use in translating sequences +# (done in script 3) by checking stop codons used at the end of the input CDS, as well as determining +# if there is a significant number of in-frame stop codons (>5%). It outputs the results of this +# stop-codon analysis into the gcode_output.tsv file, which the user can fill in with desired genetic +# codes to use in translation. If genetic codes were input originally (using the --genetic_code argument in +# wrapper.py), then no action is needed here. This script is intended to be run as part of the PhyloToL 6 +# Part 1 pipeline using the script wrapper.py. +#Dependencies import argparse, os, sys from argparse import RawTextHelpFormatter,SUPPRESS from Bio import SeqIO @@ -249,4 +246,4 @@ def main(): print (color.BOLD+'\nNext Script is: '+color.PURPLE+' 3g_GCodeTranslate.py\n\n'+color.END) -main() \ No newline at end of file +main()