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Updating header in 3_GCodeTranslate.py

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Auden Cote-L'Heureux 2024-01-26 11:35:25 -05:00 committed by GitHub
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PTL1/Genomes/Scripts/3_GCodeTranslate.py
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@ -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