saving work for mcsm_na

dynamut/run_results.py

@@ -23,8 +23,10 @@ datadir = homedir + '/git/Data'
 indir = datadir + '/' + drug + '/input'
 outdir = datadir + '/' + drug + '/output'
 
+# batch 1: 00.txt
 my_url_file =  outdir + '/dynamut_temp/dynamut_result_url_gid_b1.txt'
 my_suffix = 'gid_b1'
+
 #==========================
 # CALL: get_results() 
 # Data: gid+streptomycin

mcsm_na/examples.py

@@ -9,7 +9,7 @@ import os
 homedir = os.path.expanduser('~')
 os.chdir (homedir + '/git/LSHTM_analysis/mcsm_na')
 from submit_mcsm_na import *
-from get_results import *
+from get_results_mcsm_na import *
 #%%#####################################################################
 #EXAMPLE RUN for different stages
 #=====================

mcsm_na/get_results.py

@@ -1,53 +0,0 @@
-#!/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
-#%%#####################################################################
-
-def get_results(url_file, host_url, output_dir, outfile_suffix):
-    # initilialise empty df
-    #mcsm_na_results_out_df = pd.DataFrame()
-    with open(url_file, 'r') as f:
-        for count, line in enumerate(f):
-            line = line.strip()
-            print('URL no.', count+1, '\n', line)
-            
-            #============================
-            # Writing results file: csv
-            #============================                   
-            mcsm_na_results_dir = output_dir + '/mcsm_na_results'
-            if not os.path.exists(mcsm_na_results_dir):
-                print('\nCreating dir: mcsm_na_results within:', output_dir )
-                os.makedirs(mcsm_na_results_dir)   
-                          
-        # TODO: add as a cmd option
-            # Download .tar.gz file
-            prediction_number = re.search(r'([0-9]+\.[0-9]+$)', line).group(0)
-            print('CHECK prediction no:', prediction_number)
-            txt_url = f"{host_url}/mcsm_na/static/results/" + prediction_number + '.txt'
-            print('CHECK txt url:', txt_url)
-            
-            out_filename = mcsm_na_results_dir + '/' + outfile_suffix + '_output_' + prediction_number + '.txt'
-            response_txt = requests.get(txt_url, stream = True)
-            if response_txt.status_code == 200:
-                print('\nDownloading .txt:', txt_url
-                      , '\n\nSaving file as:', out_filename)
-                with open(out_filename, 'wb') as f:
-                    f.write(response_txt.raw.read())
-   
-#%%##################################################################### 
-

mcsm_na/run_submit.py

@@ -8,7 +8,7 @@ Created on Fri Feb 12 12:15:26 2021
 #%% load packages
 import os
 homedir = os.path.expanduser('~')
-os.chdir (homedir + '/git/LSHTM_analysis/dynamut')
+os.chdir (homedir + '/git/LSHTM_analysis/mcsm_na')
 from submit_mcsm_na import *
 ########################################################################
 # variables
@@ -26,10 +26,15 @@ outdir = datadir + '/' + drug + '/output'
 my_nuc_type = 'RNA'
 my_pdb_file = indir + '/gid_complex.pdb'
 
-# batch 1: 00.txt
+# batch 1: 00.txt: # RAN: 11 Feb, ~17:37, RETRIEVED: 15 Feb~ 12:18
-my_mutation_list = outdir + '/snp_batches/20/snp_batch_00.txt'
+#my_mutation_list = outdir + '/snp_batches/20/snp_batch_00.txt'
-my_suffix = 'gid_b1'
+#my_suffix = 'gid_b1'
-#RAN: 11 Feb, ~17:37
+
+
+# batch 2: 01.txt
+my_mutation_list = outdir + '/snp_batches/20/snp_batch_01.txt'
+my_suffix = 'gid_b2'
+# RAN: 15 Feb: 12:18
 
 #==========================
 # CALL: submit_mcsm_na()