r27354 - /trunk/lib/sequence_alignment/align_protein.py -- January 29, 2015 - 15:37

Author: bugman
Date: Thu Jan 29 15:37:23 2015
New Revision: 27354

URL: http://svn.gna.org/viewcvs/relax?rev=27354&view=rev
Log:
The protein pairwise sequence alignment function now returns the alignment 
score.

This is in the lib.sequence_alignment.align_protein.align_pairwise() 
function.  The score from the
Needleman-Wunsch sequence alignment algorithm is simply passed along.


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=27354&r1=27353&r2=27354&view=diff
==============================================================================
--- trunk/lib/sequence_alignment/align_protein.py       (original)
+++ trunk/lib/sequence_alignment/align_protein.py       Thu Jan 29 15:37:23 
2015
@@ -52,8 +52,8 @@
     @type end_gap_extend_penalty:       float
     @keyword verbosity:                 The level of verbosity.  Setting 
this to zero silences all printouts.
     @type verbosity:                    int
-    @return:                            The two alignment strings and the 
gap matrix.
-    @rtype:                             str, str, numpy rank-2 int array
+    @return:                            The alignment score, two alignment 
strings and the gap matrix.
+    @rtype:                             float, str, str, numpy rank-2 int 
array
     """
 
     # Checks.
@@ -87,7 +87,7 @@
 
     # The alignment.
     if algorithm == 'NW70':
-        align1, align2, gaps = needleman_wunsch_align(sequence1, sequence2, 
sub_matrix=sub_matrix, sub_seq=sub_seq, gap_open_penalty=gap_open_penalty, 
gap_extend_penalty=gap_extend_penalty, 
end_gap_open_penalty=end_gap_open_penalty, 
end_gap_extend_penalty=end_gap_extend_penalty)
+        score, align1, align2, gaps = needleman_wunsch_align(sequence1, 
sequence2, sub_matrix=sub_matrix, sub_seq=sub_seq, 
gap_open_penalty=gap_open_penalty, gap_extend_penalty=gap_extend_penalty, 
end_gap_open_penalty=end_gap_open_penalty, 
end_gap_extend_penalty=end_gap_extend_penalty)
 
     # Final printout.
     if verbosity:
@@ -102,4 +102,4 @@
         sys.stdout.write("\n\n")
 
     # Return the results.
-    return align1, align2, gaps
+    return score, align1, align2, gaps