diff --git a/PTL1/Transcriptomes/Scripts/7a_FinalizeName.py b/PTL1/Transcriptomes/Scripts/7a_FinalizeName.py index 5d1e02e..6e14360 100644 --- a/PTL1/Transcriptomes/Scripts/7a_FinalizeName.py +++ b/PTL1/Transcriptomes/Scripts/7a_FinalizeName.py @@ -1,34 +1,10 @@ -#!/usr/bin/env python3.5 +# Last updated Sept 29th, 2023 +# Authors: Xyrus Maurer-Alcala and Auden Cote-L'Heureux -##__Updated__: 9_29_2023 by Auden Cote-L'Heureux -##__Author__: Xyrus Maurer-Alcala; maurerax@gmail.com -##__Usage__: python 6_FilterPartials.py --help - -################################################################################################## -## This script is intended to rename the outputs of the FilterPartials script ## -## to a given 10-character that is used in the Katz lab Phylogenomic Tree building methods ## -## ## -## Prior to r`ning 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 ## -## 6. You either know (or have inferred) the genetic code of the organism ## -## 7. You have translated the sequences and checked for the data in the RemovePartials folder ## -## 8. Partial sequences have been removed from the transcriptomic data sets ## -## ## -## 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: ## -## NONE! You're FINISHED! :D ## -## ## -################################################################################################## +# This script does not process sequence data in any way. It only renames the outputs of +# script 6 to the 10-digit taxon code which prefixes the file names, and then moves output +# 'ReadyToGo' files into a separate folder. It is intended to be run as part of the PhyloToL +# 6 Part 1 pipeline using the script wrapper.py. import argparse, os, sys from argparse import RawTextHelpFormatter,SUPPRESS @@ -297,4 +273,4 @@ def main(): next_script(args) -main() \ No newline at end of file +main()