From fa20addc6e10578ec89c7a6cea3ec33efc753353 Mon Sep 17 00:00:00 2001 From: Auden Cote-L'Heureux <52716489+AudenCote@users.noreply.github.com> Date: Fri, 26 Jan 2024 11:35:25 -0500 Subject: [PATCH] Updating header in 3_GCodeTranslate.py --- PTL1/Genomes/Scripts/3_GCodeTranslate.py | 29 ++++++++---------------- 1 file changed, 10 insertions(+), 19 deletions(-) diff --git a/PTL1/Genomes/Scripts/3_GCodeTranslate.py b/PTL1/Genomes/Scripts/3_GCodeTranslate.py index 6b97409..92c9593 100644 --- a/PTL1/Genomes/Scripts/3_GCodeTranslate.py +++ b/PTL1/Genomes/Scripts/3_GCodeTranslate.py @@ -1,23 +1,14 @@ -#!/usr/bin/env python3.5 - -##__Updated__: 19_09_2017 -##__Author__: Xyrus Maurer-Alcala; maurerax@gmail.com -##__Usage__: python 3g_GCodeTranslate.py --help - - -############################################################################## -## ## -## Translates CDSs sequences using the Provided Genetic Code. ## -## ## -## NOTE: ## -## No provided input for genetic code results in Translation with the ## -## UNIVERSAL genetic code (as default) ## -## ## -## E-mail Xyrus (author) for help if needed: maurerax@gmail.com ## -## ## -############################################################################## +# Last updated Sept 2017 +# Author: Xyrus Maurer-Alcala +# Translates CDSs sequences using the provided genetic code (as read from the gcode_output.tsv +# file output by script 2, and filled in by the user if they did not pass genetic code +# assignments to the --genetic_code argument to wrapper.py. The genetic code tables can be found +# at the top of the script. In-frame stop codons are replaced with a * (the process is much simpler +# here than in the transcriptomes pipeline). This script is intended to be run using the script +# wrapper.py as part of the PhyloToL 6 Part 1 pipeline. +#Dependencies import argparse, os, sys from argparse import RawTextHelpFormatter,SUPPRESS from Bio import SeqIO @@ -394,4 +385,4 @@ def main(): print (color.BOLD+'Next Script is: '+color.PURPLE+' 4g_CountOgsUsearch.py\n\n'+color.END) -main() \ No newline at end of file +main()