renaming file

dynamut/run_submit_dynamut.py

@@ -1,58 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-"""
-Created on Wed Aug 19 14:33:51 2020
-
-@author: tanu
-"""
-#%% load packages
-import os
-homedir = os.path.expanduser('~')
-os.chdir (homedir + '/git/LSHTM_analysis/dynamut')
-from submit import *
-########################################################################
-# variables
-my_host = 'http://biosig.unimelb.edu.au'
-my_prediction_url = f"{my_host}/dynamut/prediction_list"
-print(my_prediction_url)
-
-# TODO: add cmd line args
-#gene = 'gid'
-drug = 'streptomycin'
-datadir = homedir + '/git/Data'
-indir = datadir + '/' + drug + '/input'
-outdir = datadir + '/' + drug + '/output'
-
-my_chain = 'A'
-my_email = 'tanushree.tunstall@lshtm.ac.uk'
-
-my_pdb_file = indir + '/gid_complex.pdb'
-
-# batch 1: 00.txt
-#my_mutation_list =outdir + '/snp_batches/50/snp_batch_00.txt'
-#my_suffix = 'gid_b1'
-#RAN: 11 Feb, ~14:00 pm * RETRIEVED
-
-# batch 2: 01.txt
-#my_mutation_list = outdir + '/snp_batches/50/snp_batch_01.txt'
-#my_suffix = 'gid_b2'
-#RAN: 12 Feb, ~10:00 am, AWAITING
-
-# batch 3: 02.txt
-my_mutation_list = outdir + '/snp_batches/50/snp_batch_02.txt'
-my_suffix = 'gid_b3'
-#RAN: 12 Feb, ~12:40 pm, AWAITING
-
-#==========================
-# CALL: submit_dynamut() 
-# Data: gid+streptomycin
-#==========================
-submit_dynamut(host_url = my_host
-               , pdb_file = my_pdb_file
-               , mutation_list = my_mutation_list
-               , chain = my_chain
-               , email_address = my_email
-               , prediction_url = my_prediction_url
-               , output_dir = outdir
-               , outfile_suffix = my_suffix) 
-#%%#####################################################################