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Updating headers in 5_GCodeTranslate.py

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Auden Cote-L'Heureux 2024-01-26 10:39:33 -05:00 committed by GitHub
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PTL1/Transcriptomes/Scripts/5_GCodeTranslate.py
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#!/usr/bin/env python3.5 # Last updated Sept 2023
# Authors: Xyrus Maurer-Alcala and Auden Cote-L'Heureux
##__Updated__: 20_09_2017 # This script is intended to translate nucleotide sequences. It does this using
##__Author__: Xyrus Maurer-Alcala; maurerax@gmail.com # the gcode_output.tsv file output by script 4 and containing in-frame stop codon
##__Usage__: python 5_GCodeTranslate.py --help # frequencies. The user can use this stop codon information to fill in the last
# column in this file with the genetic code for each taxon. If the user input a
# genetic code or list of genetic codes to script 1, then the gcode_output.tsv will
# be filled automatically. sequences are translated using the Diamond BLASTp results
# from OG assignment as a starting point for determining coding sequence boundaries.
# The first in-frame start codon (if the 5’ boundary of the BLASTp hit is not at a start codon)
# and last in-frame stop codon (using the assigned genetic code) outside of these bounds
# are found, while ensuring that in-frame stop codons are not introduced (given the nature
# of transcriptomic data, poor genetic code assignment or low-quality/partial data can
# interfere with this process).
# This script is intended to be run using the wrapper.py as part of the PhyloToL 6 Part 1
# pipeline. It requires that the setup of the 'Output' folder be that as output by script 4
# of this pipeline.
########################################################################################## #Dependencies
## 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 1_ContigFiltStats.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 ##
## 6. You either know (or have inferred) the genetic code of the organism ##
## ##
## E-mail Xyrus (author) for help if needed: maurerax@gmail.com ##
## ##
## Next Script(s) to Run: ##
## 6_FilterPatials.py (in FinalizeTranscripts Folder) ##
## ##
##########################################################################################
import argparse, os, re, sys import argparse, os, re, sys
from argparse import RawTextHelpFormatter,SUPPRESS from argparse import RawTextHelpFormatter,SUPPRESS