Merge branch 'master' of https://github.com/labstructbioinf/PiPred

Author: Jan Ludwiczak

pipred.py

@@ -4,7 +4,7 @@
 import sys
 import random
 import numpy as np
-from utils import enc_seq_onehot, enc_pssm, is_fasta, get_pssm_sequence, PiPred_Model, decode
+from utils import enc_seq_onehot, enc_pssm, is_fasta, get_pssm_sequence, PiPred_Model, decode,exit
 import keras.backend as K
 
 # cx_freeze specific
@@ -91,9 +91,13 @@
     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:
-        print("ERROR: Malformed PSSM file for entry %s!" % entry)
-        exit()
+        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...")