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Updating header in 2_GCodeEval.py

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Auden Cote-L'Heureux 2024-01-26 11:30:22 -05:00 committed by GitHub
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PTL1/Genomes/Scripts/2_GCodeEval.py
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@ -1,18 +1,15 @@
#!/usr/bin/env python3.5 # Last updated Sept 2017
# Author: Xyrus Maurer-Alcala
##__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. #
# #
#############################################################################################
# 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 import argparse, os, sys
from argparse import RawTextHelpFormatter,SUPPRESS from argparse import RawTextHelpFormatter,SUPPRESS
from Bio import SeqIO from Bio import SeqIO