r27308 - /trunk/lib/sequence_alignment/align_protein.py -- January 26, 2015 - 15:20

Author: bugman
Date: Mon Jan 26 15:20:09 2015
New Revision: 27308

URL: http://svn.gna.org/viewcvs/relax?rev=27308&view=rev
Log:
Python 3 fix for the lib.sequence_alignment.align_protein module.

The string.upper() function no longer exists.


Modified:
    trunk/lib/sequence_alignment/align_protein.py

Modified: trunk/lib/sequence_alignment/align_protein.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/lib/sequence_alignment/align_protein.py?rev=27308&r1=27307&r2=27308&view=diff
==============================================================================
--- trunk/lib/sequence_alignment/align_protein.py       (original)
+++ trunk/lib/sequence_alignment/align_protein.py       Mon Jan 26 15:20:09 
2015
@@ -23,7 +23,6 @@
 """General sequence alignment functions."""
 
 # Python module imports.
-from string import upper
 import sys
 
 # relax module imports.
@@ -64,8 +63,8 @@
         raise RelaxError("The substitution matrix '%s' is unknown, it must 
be one of %s." % (matrix, allowed_matrices))
 
     # Capitalise the sequences.
-    sequence1 = upper(sequence1)
-    sequence2 = upper(sequence2)
+    sequence1 = sequence1.upper()
+    sequence2 = sequence2.upper()
 
     # Initial printout.
     sys.stdout.write("\nPairwise protein alignment.\n")