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Headers in 4_InFrameStopCodonEstimator.py

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PTL1/Transcriptomes/Scripts/4_InFrameStopCodonEstimator.py
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#!/usr/bin/env python # Last updated Sept 2023
# Authors: Xyrus Maurer-Alcala and Auden Cote-L'Heureux
##__Updated__: 18_08_2017
##__Author__: Xyrus Maurer-Alcala; maurerax@gmail.com
##__Usage__: python 4_InFrameStopFreq.py --help
##########################################################################################
## This script is intended to aid in identifying the genetic code of the data given ##
## ##
## Prior to running this script, ensure the following: ##
## ##
## 1. You have assembled your transcriptome and COPIED the 'assembly' file ##
## (contigs.fasta, or scaffolds.fasta) to the PostAssembly Folder ##
## 2. Removed small sequences (usually sequences < 300bp) with ContigFilterPlusStats.py ##
## 3. Removed SSU/LSU sequences from your Fasta File ##
## 4. Classified your sequences as Strongly Prokaryotic/Eukaryotic or Undetermined ##
## 5. Classified the Non-Strongly Prokaryotic sequences into OGs ##
## ##
## COMMAND Example Below ##
## Extra Notes at Bottom of Script ##
## ##
## E-mail Xyrus (author) for help if needed: maurerax@gmail.com ##
## ##
## Next Script(s) to Run: ##
## 5_GCodeTranslate.py ##
## ##
##########################################################################################
# This script is intended to aid in identifying the genetic code of assembled
# transcripts by similarity searching against a reference database of representative
# sequences (Databases/RepEukProts) and calculating and reporting in-frame stop coding
# frequencies in all reading frames; it then reports these frequencies in a spreadsheet
# (gcodes_output.tsv) for the user to inspect in deciding which genetic codes to use,
# if unsure. This step can be skipped if genetic codes were input from the beginning. This
# script should be run through the PhyloToL 6 Part 1 pipeline using the script wrapper.py.
import argparse, os, sys import argparse, os, sys
from argparse import RawTextHelpFormatter,SUPPRESS from argparse import RawTextHelpFormatter,SUPPRESS