open files in binary mode for pickle

Author: RMeli

Diff for: clustering.py

@@ -318,15 +318,15 @@ def computeLigandSimilarity(target_names, fname):
     ligand_threshold = args.ligand_similarity #this actually is a sim
 
     if args.cpickle:
-        with open(args.cpickle, 'r') as file:
+        with open(args.cpickle, 'rb') as file:
             (distanceMatrix, target_names,ligandsim) = pickle.load(file)
     elif args.pdbfiles:
         if args.verbose: print("reading pdbs...")
         target_names, targets = readPDBfiles(args.pdbfiles)
         if args.verbose: print("calculating distance matrix...")
         distanceMatrix = calcDistanceMatrix(targets)
         ligandsim = computeLigandSimilarity(target_names, args.pdbfiles) #returns similarity matrix indexed according to target_names
-        pickle.dump((distanceMatrix, target_names, ligandsim), open(args.pdbfiles+'.pickle','w'),-1)
+        pickle.dump((distanceMatrix, target_names, ligandsim), open(args.pdbfiles+'.pickle','wb'),-1)
     else:
         exit('error: need --cpickle or --pdbfiles to compute target distance matrix')
     if args.verbose: print('Number of targets: {}'.format(len(target_names)))

Diff for: combine_rows.py

@@ -44,4 +44,4 @@
             print("Missing ligand_sim for",targets[i],targets[j])
 
 
-pickle.dump((m, target_names, lm), open('matrix.pickle','w'),-1)
+pickle.dump((m, target_names, lm), open('matrix.pickle','wb'),-1)