added mcsm_na scripts to submit batches of 20

mcsm_na/examples.py

@@ -0,0 +1,56 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Fri Feb 12 12:15:26 2021
+
+@author: tanu
+"""
+import os
+homedir = os.path.expanduser('~')
+os.chdir (homedir + '/git/LSHTM_analysis/mcsm_na')
+from submit_mcsm_na import *
+from get_results import *
+#%%#####################################################################
+#EXAMPLE RUN for different stages
+#=====================
+# STAGE: submit_mcsm_na.py
+#=====================
+my_host = 'http://biosig.unimelb.edu.au'
+my_prediction_url = f"{my_host}/mcsm_na/run_prediction_list"
+print(my_prediction_url)
+
+my_outdir = homedir + '/git/LSHTM_analysis/mcsm_na'
+
+my_pdb_file = homedir + '/git/Data/streptomycin/input/gid_complex.pdb'
+my_mutation_list = homedir + '/git/LSHTM_analysis/mcsm_na/test_snps_b1.csv'
+my_suffix = 'gid_test_b1'
+
+#----------------------------------------------
+# example 1: 2 snps in a file
+#----------------------------------------------
+submit_mcsm_na(host_url = my_host
+, pdb_file = my_pdb_file
+, mutation_list = my_mutation_list
+, nuc_type = 'RNA'
+, prediction_url = my_prediction_url
+, output_dir = my_outdir
+, outfile_suffix = my_suffix) 
+#%%###################################################################
+
+#=====================
+# STAGE: get_results.py
+#=====================
+my_host = 'http://biosig.unimelb.edu.au'
+my_outdir = homedir + '/git/LSHTM_analysis/mcsm_na'
+
+#----------------------------------------------
+# example 1: single url in a single file
+#----------------------------------------------
+my_url_file_single = homedir + '/git/LSHTM_analysis/mcsm_na/mcsm_na_temp/mcsm_na_result_url_gid_test_b1.txt'
+print(my_url_file_single)
+my_suffix = 'single'
+
+get_results(url_file  = my_url_file_single
+            , host_url = my_host
+            , output_dir = my_outdir
+            , outfile_suffix = my_suffix)