renamed file run_submit to run_submit_dynamut

dynamut/run_submit_dynamut.py

@@ -0,0 +1,58 @@
+#!/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) 
+#%%#####################################################################