Snippets

Biosig Lab Submission of prediction job for list of mutations - DynaMut2

Updated by Carlos Miranda Rodrigues

File list_mutations_job_submission.py Modified

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 import requests
 import sys
 
-URL = "http://biosig.unimelb.edu.au/dynamut2/api/prediction_list"
+URL = "https://biosig.lab.uq.edu.au/dynamut2/api/prediction_list"
 
 def main(args):
     pdb_file = args.pdb_file
Updated by Carlos Miranda Rodrigues

File list_mutations_job_submission.py Modified

  • Ignore whitespace
  • Hide word diff
 import requests
 import sys
 
-URL = "http://biosig.unimelb.edu.au/dynamut2app/api/prediction_list"
+URL = "http://biosig.unimelb.edu.au/dynamut2/api/prediction_list"
 
 def main(args):
     pdb_file = args.pdb_file
Updated by Carlos Miranda Rodrigues

File list_mutations_job_submission.py Modified

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     return True
 
 if __name__ == "__main__":
-    parser = argparse.ArgumentParser(description='Job submission for single prediction - DynaMut2')
+    parser = argparse.ArgumentParser(description='Job submission for list prediction - DynaMut2')
     parser.add_argument('--pdb_file', dest='pdb_file', type=file, help='PDB file', required=False, default=None)
     parser.add_argument('--pdb_code', dest='pdb_code', type=str, help='4-digit PDB code', required=False, default=None)
     parser.add_argument('--mutations_list', dest='mutations_list', type=file, help='.txt or .csv file with mutation list. One mutation code per line (aaFrom + residueNumber + aaTo).', required=True)
Created by Carlos Miranda Rodrigues

File list_mutations_job_submission.py Added

  • Ignore whitespace
  • Hide word diff
+import argparse
+import requests
+import sys
+
+URL = "http://biosig.unimelb.edu.au/dynamut2app/api/prediction_list"
+
+def main(args):
+    pdb_file = args.pdb_file
+    mutations_list = args.mutations_list
+
+    fs = {"pdb_file": pdb_file, "mutations_list":mutations_list}
+    
+    req = requests.post(URL, files=fs, data={})
+    print(req.json())
+    return True
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description='Job submission for single prediction - DynaMut2')
+    parser.add_argument('--pdb_file', dest='pdb_file', type=file, help='PDB file', required=False, default=None)
+    parser.add_argument('--pdb_code', dest='pdb_code', type=str, help='4-digit PDB code', required=False, default=None)
+    parser.add_argument('--mutations_list', dest='mutations_list', type=file, help='.txt or .csv file with mutation list. One mutation code per line (aaFrom + residueNumber + aaTo).', required=True)
+    
+    args = parser.parse_args()
+    if args.pdb_code == None and args.pdb_file == None:
+        print('usage: main.py [-h] [--pdb_file PDB_FILE] [--pdb_code PDB_CODE]')
+        print('[--mutations_list MUTATIONS_LIST]')
+        print('main.py: error: missing arguments: Please provide --pdb_file or --pdb_code')
+        sys.exit(1)
+    main(args)
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