saving work in dynamut submit

dynamut/submit.py

@@ -0,0 +1,84 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Wed Aug 19 14:33:51 2020
+
+@author: tanu
+"""
+#%% load packages
+import os,sys
+import subprocess
+import argparse
+import requests
+import re
+import time
+from bs4 import BeautifulSoup
+import pandas as pd
+from pandas.api.types import is_string_dtype
+from pandas.api.types import is_numeric_dtype
+#%%
+host = 'http://biosig.unimelb.edu.au'
+prediction_url = f"{host}/dynamut/prediction_list"
+print(prediction_url)
+
+#%%
+#def format_data(data_file):
+   
+#%% request calculation (no def)
+output_dir = "/home/tanu/git/LSHTM_analysis/dynamut"
+gene_name = 'gid'
+with open("/home/tanu/git/Data/streptomycin/input/gid_complex.pdb", "rb") as pdb_file, open ("/home/tanu/git/LSHTM_analysis/dynamut/snp_test2.csv") as mutation_list:
+        files = {"wild": pdb_file
+                 , "mutation_list": mutation_list}
+        body = {"chain": 'A'
+                , "email": 'tanushree.tunstall@lshtm.ac.uk'}
+
+        response = requests.post(prediction_url, files = files, data = body)
+        print(response.status_code)
+        if response.history:
+            print('PASS: valid mutation submitted. Fetching result url')
+            url_match = re.search('/dynamut/results_prediction/.+(?=")', response.text)
+            url = host + url_match.group()
+            print(url)
+            #===============
+            # writing file: result urls
+            #===============
+            out_url_file = output_dir + '/' + gene_name.lower() + '_snp_batch' + '_result_url.txt'
+            print(out_url_file)
+            myfile = open(out_url_file, 'a')    
+            myfile.write(url + '\n')
+            myfile.close()
+        else:
+            print('ERROR: invalid mutation! Wild-type residue doesn\'t match pdb file.'
+                 , '\nSkipping to the next mutation in file...')
+             #===============
+             # writing file: invalid mutations
+             #===============
+            out_error_file = output_dir + '/' + gene_name.lower() + '_errors.txt'
+            failed_muts = open(out_error_file, 'a')    
+            failed_muts.write(mutation_list + '\n')
+            failed_muts.close()
+
+#%%
+def request_calculation(pdb_file, mutation_list, chain, my_email, prediction_url
+                        #, output_dir, gene_name
+                        , url_file):
+    """
+    Makes a POST request for a ligand affinity prediction.
+
+    @param pdb_file: valid path to pdb structure
+    @type string
+    
+    @param mutation_list: list of mutations (1 per line) of the format: {WT}<POS>{Mut}
+	@type string
+	
+    @param chain: single-letter(caps)
+	@type chr
+
+	@param prediction_url: dynamut url for prediction
+	@type string
+       
+    @return response object
+    @type object
+    """
+#====================