bug fix

Author: olekwk

pipred.py

@@ -88,16 +88,14 @@
         exit()
     try:
         parsed_pssm = np.genfromtxt(pssm_fn, skip_header=3, skip_footer=5, usecols=(i for i in range(2, 22)))
+        if parsed_pssm.shape[0] == len(seq) - 2:
+            parsed_pssm = np.genfromtxt(pssm_fn, skip_header=3, skip_footer=3, usecols=(i for i in range(2, 22)))
+   
     except ValueError:
         print("ERROR: Malformed PSSM file for entry %s!" % entry)
         exit()
 
-    if not parsed_pssm.shape[0] == len(seq) and parsed_pssm.shape[1] == 20:
-        if parsed_pssm.shape[0] == len(seq)-2:
-            parsed_pssm = np.genfromtxt(pssm_fn, skip_header=3, skip_footer=3, usecols=(i for i in range(2, 22)))
-        else:
-            print("ERROR: Malformed PSSM file for entry %s!" % entry)
-            exit()
+
     pssm_files.append(pssm_fn)
 
 print("Encoding sequences...")

utils.py

@@ -71,12 +71,10 @@ def enc_pssm(pssm_file, pad_length=None, pad_left=0):
     return pssm_matrix
 
 # Decodes predictions (takes into the account padding of sequence)
-def decode(pred, enc_seq):
-    decoded_pred = []
-    for pos_pred, pos_seq in zip(pred, enc_seq):
-        if not np.array_equal(pos_seq, np.zeros(40)):
-            decoded_pred.append(pos_pred)
-    return np.asarray(decoded_pred)
+def decode(pred, enc_sec):
+    return pred[np.any(enc_sec, axis=-1), :]
+
+
 
 # Pipred model architecture
 def PiPred_Model():