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Updating header in wrapper.py

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Auden Cote-L'Heureux 2024-01-26 11:42:05 -05:00 committed by GitHub
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PTL1/Genomes/Scripts/wrapper.py
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@ -1,3 +1,16 @@
# Last updated Sept 2023
# Author: Auden Cote-L'Heureux
# This script is a WRAPPER for the PhyloToL Part 1 GENOMES pipeline. Users should
# use this script to run the pipeline, rather than running any of the sub-scripts (number 1a through 5b)
# independently. To run an individual step in the pipeline, use --script X where X is the number (1 through 5).
# To run multiple sets (usually all of them), use --first script 1 --last_script 5, or whichever first
# and last scripts are desired. Run "python wrapper.py --help" for details on how to run this script. Before
# running this script ensure that the databases are correctly located and named, and that input CDS are named
# in the format Op_me_Hsap_GenBankCDS.fasta, where Op_me_Hsap can be replaced with any 10-digit sample
# identifier.
import os, sys, re
import argparse
import CheckSetup
@ -10,7 +23,7 @@ def get_args():
description = "Updated January 19th, 2023 by Auden Cote-L'Heureux. Link to GitHub: https://github.com/AudenCote/PhyloToL_v6.0"
)
parser.add_argument('-s', '--script', default = -1, type = int, choices = { 1, 2, 3, 4, 5, 6 }, help = 'Script to run if you are only running one script')
parser.add_argument('-s', '--script', default = -1, type = int, choices = { 1, 2, 3, 4, 5 }, help = 'Script to run if you are only running one script')
parser.add_argument('-1', '--first_script', default = -1, type = int, choices = { 1, 2, 3, 4 }, help = 'First script to run')
parser.add_argument('-2', '--last_script', default = -1, type = int, choices = { 2, 3, 4, 5 }, help = 'First script to run')
parser.add_argument('-c', '--cds', type = str, help = 'Path to a folder of nucleotide CDS. Each file name should start with a unique 10 digit code, and end in "_GenBankCDS.fasta", E.g. Op_me_hsap_GenBankCDS.fasta')