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PTL1/Transcriptomes/Scripts/3_AssignOGs.py
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#!/usr/bin/env python3.5
# Last updated Sept 2023
# Authors: Xyrus Maurer-Alcala and Auden Cote-L'Heureux
##__Updated__: 16_10_2017
##__Author__: Xyrus Maurer-Alcala; maurerax@gmail.com
##__Usage__: python 3_CountOGsDiamond.py --help
##########################################################################################
## This script is intended to classify the STRONGLY Eukaryotic and UNDETERMINED/UNKNOWN ##
## contigs into different OGs (e.g. orthologous gene-families) ##
## ##
## For more info about the OGs, check out: OrthoMCL.org ##
## ##
## 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 ##
## ##
## E-mail Xyrus (author) for help if needed: maurerax@gmail.com ##
## ##
## Next Script(s) to Run: ##
## 4_StopFrequency.py ##
## ##
##########################################################################################
# This script classifies assembled transcripts into gene families by
# similarity-searching using Diamond against a reference database of
# gene families. We provide the Hook database on the GitHub, but this
# may be replaced with a custom reference database by REPLACING the
# .dmnd and .fasta files in the Databases/db_OG folder. This script
# is intended to be run as part of the PhyloToL 6 Part 1 pipeline using
# the script wrapper.py.
import argparse, os, sys, re
from argparse import RawTextHelpFormatter,SUPPRESS