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Updating header in 5a_FinalizeName.py

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Auden Cote-L'Heureux 2024-01-26 11:37:19 -05:00 committed by GitHub
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1 changed files with 6 additions and 30 deletions
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PTL1/Genomes/Scripts/5a_FinalizeName.py
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#!/usr/bin/env python3.5
# Last updated 20_09_2017
# Author: Xyrus Maurer-Alcala
##__Updated__: 20_09_2017
##__Author__: Xyrus Maurer-Alcala; maurerax@gmail.com
##__Usage__: python 5g_FinalizeName.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 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 ##
## 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