added tar.gz download within get_results.py

dynamut/dynamut_results/dynamut_output_multiple.csv

@@ -1,7 +0,0 @@
-mutationinformation,ddg_dynamut,ddg_encom,ddg_mcsm,ddg_sdm,ddg_duet,dds_encom
-G13V,0.006 kcal/mol (Stabilizing),-0.053 kcal/mol (Destabilizing),-0.261 kcal/mol (Destabilizing),-0.120 kcal/mol (Destabilizing),0.120 kcal/mol (Stabilizing),0.066 kcal.mol-1.K-1 (Increase of molecule flexibility)
-A19T,-0.077 kcal/mol (Destabilizing),0.224 kcal/mol (Destabilizing),-0.631 kcal/mol (Destabilizing),-2.620 kcal/mol (Destabilizing),-0.758 kcal/mol (Destabilizing),-0.280 kcal.mol-1.K-1 (Decrease of molecule flexibility)
-I4N,-0.239 kcal/mol (Destabilizing),-0.720 kcal/mol (Destabilizing),-0.728 kcal/mol (Destabilizing),-0.550 kcal/mol (Destabilizing),-0.461 kcal/mol (Destabilizing),0.900 kcal.mol-1.K-1 (Increase of molecule flexibility)
-P3S,0.727 kcal/mol (Stabilizing),0.334 kcal/mol (Destabilizing),-0.672 kcal/mol (Destabilizing),0.010 kcal/mol (Stabilizing),-0.252 kcal/mol (Destabilizing),-0.418 kcal.mol-1.K-1 (Decrease of molecule flexibility)
-F12S,-0.270 kcal/mol (Destabilizing),0.048 kcal/mol (Destabilizing),-1.028 kcal/mol (Destabilizing),-0.930 kcal/mol (Destabilizing),-0.993 kcal/mol (Destabilizing),-0.060 kcal.mol-1.K-1 (Decrease of molecule flexibility)
-A19V,2.389 kcal/mol (Stabilizing),0.450 kcal/mol (Destabilizing),0.659 kcal/mol (Stabilizing),-0.170 kcal/mol (Destabilizing),1.040 kcal/mol (Stabilizing),-0.562 kcal.mol-1.K-1 (Decrease of molecule flexibility)

dynamut/examples.py

@@ -61,7 +61,7 @@ get_results(url_file  = my_url_file_multiple
 # example 2: single url in a file
 #----------------------------------------------
 my_url_file_single = homedir + '/git/LSHTM_analysis/dynamut/dynamut_temp/dynamut_result_url_batch_single.txt'
-print(my_url_file_multiple)
+print(my_url_file_single)
 my_suffix = 'single'
 
 get_results(my_url_file_single
@@ -69,3 +69,18 @@ get_results(my_url_file_single
             , output_dir = my_outdir
             , outfile_suffix = my_suffix)
 #%%###################################################################
+url = 'http://biosig.unimelb.edu.au/dynamut/results_prediction/161296287365'
+host_url = 'http://biosig.unimelb.edu.au'
+prediction_number = re.search(r'([0-9]+$)', url).group(0)
+print(prediction_number)
+dynamut_results_dir = '/home/tanu/git/LSHTM_analysis/dynamut/dynamut_results'
+tgz_url = f"{host_url}/dynamut/results_file/results_" + prediction_number + '.tar.gz'
+print(tgz_url)
+outfile_suffix = 'foo'
+
+
+target_path = dynamut_results_dir + '/' + outfile_suffix + '_results_' + prediction_number + '.tar.gz'
+response_tgz = requests.get(tgz_url, stream = True)
+if response_tgz.status_code == 200:
+    with open(target_path, 'wb') as f:
+        f.write(response_tgz.raw.read())

dynamut/get_results.py

@@ -17,6 +17,7 @@ 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
     dynamut_results_out_df = pd.DataFrame()
@@ -27,7 +28,7 @@ def get_results(url_file, host_url, output_dir, outfile_suffix):
             #batch_response = requests.get(line, headers=headers)
             batch_response = requests.get(line)
             batch_soup = BeautifulSoup(batch_response.text, features = 'html.parser')
-                                   
+                                  
             # initilialise empty df
             #dynamut_results_df = pd.DataFrame()
             for a in batch_soup.find_all('a', href=True, attrs = {'class':'btn btn-default btn-sm'}):
@@ -80,4 +81,17 @@ def get_results(url_file, host_url, output_dir, outfile_suffix):
     # build out filename
     out_filename = dynamut_results_dir + '/dynamut_output_' + outfile_suffix + '.csv'
     dynamut_results_out_df.to_csv(out_filename, index = False)
+       
+    # Download .tar.gz file
+    prediction_number = re.search(r'([0-9]+$)', line).group(0)
+    tgz_url = f"{host_url}/dynamut/results_file/results_" + prediction_number + '.tar.gz'
+    tgz_filename = dynamut_results_dir + '/' + outfile_suffix + '_results_' + prediction_number + '.tar.gz'
+    response_tgz = requests.get(tgz_url, stream = True)
+    if response_tgz.status_code == 200:
+        print('\nDownloading tar.gz file:', tgz_url
+              , '\nSaving file as:', tgz_filename)
+        with open(tgz_filename, 'wb') as f:
+            f.write(response_tgz.raw.read())
+   
 #%%#####################################################################    
+

dynamut/run_results.py

@@ -35,4 +35,5 @@ get_results(url_file  = my_url_file
            , host_url = my_host
            , output_dir = outdir
            , outfile_suffix = my_suffix)
+           
 ########################################################################