r27358 - /trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_needleman_wunsch.py -- January 29, 2015 - 15:53

Author: bugman
Date: Thu Jan 29 15:53:41 2015
New Revision: 27358

URL: http://svn.gna.org/viewcvs/relax?rev=27358&view=rev
Log:
Fixes for the unit tests of the 
_lib._sequence_alignment.test_needleman_wunsch module.

The lib.sequence_alignment.needleman_wunsch.needleman_wunsch_align() function 
now returns the
alignment score.


Modified:
    
trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_needleman_wunsch.py

Modified: 
trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_needleman_wunsch.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_needleman_wunsch.py?rev=27358&r1=27357&r2=27358&view=diff
==============================================================================
--- 
trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_needleman_wunsch.py 
      (original)
+++ 
trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_needleman_wunsch.py 
      Thu Jan 29 15:53:41 2015
@@ -41,8 +41,9 @@
         print(seq2)
 
         # Perform the alignment. 
-        align1, align2, gaps = needleman_wunsch_align(seq1, seq2, 
sub_matrix=SIMILARITY_DNA, sub_seq=SIMILARITY_DNA_SEQ, gap_open_penalty=1, 
gap_extend_penalty=1)
+        score, align1, align2, gaps = needleman_wunsch_align(seq1, seq2, 
sub_matrix=SIMILARITY_DNA, sub_seq=SIMILARITY_DNA_SEQ, gap_open_penalty=1, 
gap_extend_penalty=1)
         print("\nOut:")
+        print(score)
         print(align1)
         print(align2)
         print(gaps)
@@ -81,8 +82,9 @@
         print(seq2)
 
         # Perform the alignment. 
-        align1, align2, gaps = needleman_wunsch_align(seq1, seq2, 
sub_matrix=NUC_4_4, sub_seq=NUC_4_4_SEQ, gap_open_penalty=5, 
gap_extend_penalty=1)
+        score, align1, align2, gaps = needleman_wunsch_align(seq1, seq2, 
sub_matrix=NUC_4_4, sub_seq=NUC_4_4_SEQ, gap_open_penalty=5, 
gap_extend_penalty=1)
         print("\nOut:")
+        print(score)
         print(align1)
         print(align2)
         print(gaps)
@@ -121,8 +123,9 @@
         print(seq2)
 
         # Perform the alignment. 
-        align1, align2, gaps = needleman_wunsch_align(seq1, seq2, 
sub_matrix=NUC_4_4, sub_seq=NUC_4_4_SEQ, gap_open_penalty=5, 
gap_extend_penalty=1)
+        score, align1, align2, gaps = needleman_wunsch_align(seq1, seq2, 
sub_matrix=NUC_4_4, sub_seq=NUC_4_4_SEQ, gap_open_penalty=5, 
gap_extend_penalty=1)
         print("\nOut:")
+        print(score)
         print(align1)
         print(align2)
         print(gaps)