Revert "add parsing PSSM from custom msa"

This reverts commit 5dd98e0.

Author: Jan Ludwiczak

pipred.py

@@ -86,15 +86,11 @@
     if not get_pssm_sequence(pssm_fn) == seq:
         print("ERROR: Sequence in PSSM file does not match fasta sequence for entry %s!" % entry)
         exit()
-        try:
-            parsed_pssm = np.genfromtxt(pssm_fn, skip_header=3, skip_footer=5, usecols=(i for i in range(2, 22)))
-            if not parsed_pssm.shape[0] == len(seq):
-                parsed_pssm = np.genfromtxt(pssm_fn, skip_header=3, skip_footer=3, usecols=(i for i in range(2, 22)))
-                if not parsed_pssm.shape[0] == len(seq):
-                    raise ValueError
-        except ValueError:
-            print("ERROR: Malformed PSSM file for entry %s!" % entry)
-            exit()
+    try:
+        parsed_pssm = np.genfromtxt(pssm_fn, skip_header=3, skip_footer=5, 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: