diff --git a/PTL1/Transcriptomes/Scripts/3_AssignOGs.py b/PTL1/Transcriptomes/Scripts/3_AssignOGs.py index 74b54d1..c7ebb38 100644 --- a/PTL1/Transcriptomes/Scripts/3_AssignOGs.py +++ b/PTL1/Transcriptomes/Scripts/3_AssignOGs.py @@ -1,29 +1,14 @@ -#!/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