Author: bugman
Date: Thu Jan 22 16:56:35 2015
New Revision: 27272
URL: http://svn.gna.org/viewcvs/relax?rev=27272&view=rev
Log:
Created the Test_needleman_wunsch.test_needleman_wunsch_align_NUC_4_4 unit test.
This is in the unit test module _lib._sequence_alignment.test_needleman_wunsch.
This tests the
Needleman-Wunsch sequence alignment for two DNA sequences using the NUC 4.4
matrix.
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=27272&r1=27271&r2=27272&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 22 16:56:35 2015
@@ -60,3 +60,43 @@
for i in range(2):
for j in range(8):
self.assertEqual(gaps[i, j], real_gaps[i][j])
+
+
+ def test_needleman_wunsch_align_NUC_4_4(self):
+ """Test the Needleman-Wunsch sequence alignment for two DNA sequences
using the NUC 4.4 matrix.
+
+ From online servers, the results with a gap open penalty of 5 and gap
extend of 1 should be::
+
+ https://www.ebi.ac.uk/Tools/psa/emboss_needle/
+ EMBOSS_001 1 GAAAAAAT 8
+ | |||
+ EMBOSS_001 1 G----AAT 4
+ """
+
+ # The sequences.
+ seq1 = 'GAAAAAAT'
+ seq2 = 'GAAT'
+ print("\nIn:")
+ print(seq1)
+ 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)
+ print("\nOut:")
+ print(align1)
+ print(align2)
+ print(gaps)
+ print("\n")
+
+ # Check the alignment.
+ self.assertEqual(align1, 'GAAAAAAT')
+ self.assertEqual(align2, 'G----AAT')
+
+ # The gap matrix.
+ real_gaps = [
+ [0, 0, 0, 0, 0, 0, 0, 0],
+ [0, 1, 1, 1, 1, 0, 0, 0]
+ ]
+ for i in range(2):
+ for j in range(8):
+ self.assertEqual(gaps[i, j], real_gaps[i][j])
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