added submit_def.py with example to run batch of 50

dynamut/submit.py

@@ -44,7 +44,7 @@ out_url_file = dynamut_temp_dir + '/dynamut_result_url_batch_' + str(batch_no) +
 
    
 #%% request calculation (no def)
-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:
+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", "rb") as mutation_list:
         files = {"wild": pdb_file
                  , "mutation_list": mutation_list}
         body = {"chain": 'A'
@@ -57,6 +57,7 @@ with open("/home/tanu/git/Data/streptomycin/input/gid_complex.pdb", "rb") as pdb
             url_match = re.search('/dynamut/results_prediction/.+(?=")', response.text)
             url = host + url_match.group()
             print(url)
+            
             #===============
             # writing file: result urls
             #===============
@@ -90,7 +91,31 @@ def request_calculation(pdb_file, mutation_list
 	@param prediction_url: dynamut url for prediction
 	@type string
        
-    @return response object
+    @return txt file containing batch no. of snps processed
-    @type object
+    @type string
     """
+    
+    with open(pdb_file, "rb") as pdb_file, open (mutation_list) 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 = dynamut_temp_dir + '/dynamut_result_url_batch_' + str(batch_no) + '.txt'
+            print('Writing output url file:', out_url_file)
+            myfile = open(out_url_file, 'a')    
+            myfile.write(url)
+            myfile.close()
 #====================
+# Submit first batch

dynamut/submit_def.py

@@ -0,0 +1,116 @@
+#!/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
+#%% homedir
+homedir = os.path.expanduser('~')
+print('My homedir is:', homedir)
+#%%
+def request_calculation(pdb_file
+                        , mutation_list
+                        , batch_no
+                        , chain
+                        , my_email
+                        , prediction_url
+                        , output_dir
+                        #, gene_name
+                        #, out_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 batch_no: batch no so it can be added as a suffix to the the outfile
+	@type int
+    
+    @param chain: single-letter(caps)
+	@type chr
+
+	@param prediction_url: dynamut url for prediction
+	@type string
+       
+    @param output_dir: output dir
+	@type string
+
+    @param gene_name: name of gene
+	@type string
+    
+    #@param out_url_file: name of output file with batch no. as suffix
+	@type string
+       
+    @return txt file containing batch no. of snps processed (i.e out_url_file)
+    @type string
+    """
+    
+    with open(pdb_file, "rb") as pdb_file, open (mutation_list, "rb") as mutation_list:
+        files = {"wild": pdb_file
+                 , "mutation_list": mutation_list}
+        body = {"chain": chain
+                , "email": my_email}
+
+        response = requests.post(prediction_url, files = files, data = body)
+        print(response.status_code)
+        if response.history:
+            print('\nPASS: valid submission. Fetching result url')
+            url_match = re.search('/dynamut/results_prediction/.+(?=")', response.text)
+            url = host + url_match.group()
+            print('\nURL for snp batch no ', str(batch_no), ':', url)
+            
+            #===============
+            # writing file: result urls
+            #===============
+            dynamut_temp_dir = outdir + '/dynamut_temp'
+            if not os.path.exists(dynamut_temp_dir):
+                print('\nCreating dynamut_temp in outdir', outdir )
+                os.makedirs(dynamut_temp_dir)                    
+            
+            out_url_file = dynamut_temp_dir + '/dynamut_result_url_batch_' + str(batch_no) + '.txt'
+            print('\nWriting output url file:', out_url_file)
+            myfile = open(out_url_file, 'a')    
+            myfile.write(url)
+            myfile.close()
+#%%globals!?
+host = 'http://biosig.unimelb.edu.au'
+#prediction_url = f"{host}/dynamut/prediction_list"
+#print(prediction_url)
+
+#gene = 'gid'
+drug = 'streptomycin'
+datadir = homedir + '/git/Data'
+indir = datadir + '/' + drug + '/input'
+outdir = datadir + '/' + drug + '/output'
+#outdir = homedir + '/git/LSHTM_analysis/dynamut' # for example
+
+
+my_pdb_file = homedir + '/git/Data/streptomycin/input/gid_complex.pdb'
+my_mutation_list = homedir + '/git/Data/streptomycin/output/snp_batches/50/snp_batch_00.txt'
+my_chain = 'A'
+my_batch = 1
+#my_outfile = dynamut_temp_dir + '/dynamut_result_url_batch_' + str(batch_no) + '.txt'
+# %% call this function
+request_calculation (pdb_file = my_pdb_file
+, mutation_list = my_mutation_list
+, chain = my_chain
+, my_email = 'tanushree.tunstall@lshtm.ac.uk'
+, prediction_url = f"{host}/dynamut/prediction_list"
+, output_dir = outdir
+, batch_no = my_batch)