From df54de35891be9be6507cb26a975472e771063df Mon Sep 17 00:00:00 2001 From: Auden Cote-L'Heureux <52716489+AudenCote@users.noreply.github.com> Date: Fri, 26 Jan 2024 11:42:05 -0500 Subject: [PATCH] Updating header in wrapper.py --- PTL1/Genomes/Scripts/wrapper.py | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/PTL1/Genomes/Scripts/wrapper.py b/PTL1/Genomes/Scripts/wrapper.py index 2beacc0..3988d0b 100644 --- a/PTL1/Genomes/Scripts/wrapper.py +++ b/PTL1/Genomes/Scripts/wrapper.py @@ -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')