Author: bugman
Date: Thu Jan 29 15:52:16 2015
New Revision: 27357
URL: http://svn.gna.org/viewcvs/relax?rev=27357&view=rev
Log:
Fixes for the unit tests of the _lib._sequence_alignment.test_align_protein
module.
The Test_align_protein.test_align_pairwise_PAM250 unit test was accidentally
duplicated due to a
copy and paste error. And the
lib.sequence_alignment.align_protein.align_pairwise() function now
also returns the alignment score.
Modified:
trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_align_protein.py
Modified:
trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_align_protein.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_align_protein.py?rev=27357&r1=27356&r2=27357&view=diff
==============================================================================
--- trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_align_protein.py
(original)
+++ trunk/test_suite/unit_tests/_lib/_sequence_alignment/test_align_protein.py
Thu Jan 29 15:52:16 2015
@@ -30,57 +30,6 @@
class Test_align_protein(TestCase):
"""Unit tests for the lib.sequence_alignment.align_protein relax module."""
- def test_align_pairwise_PAM250(self):
- """Test the Needleman-Wunsch sequence alignment for two protein
sequences using the PAM250 substitution matrix.
-
- This uses the sequences:
-
- - 'IHAAEEKDWKTAYSYbgFYEAFEGYdsidspkaitslkymllckimlntpedvqalvsgkla',
- -
'LHAADEKDFKTAFSYabiggapFYEAFEGYdsvdekvsaltalkymllckvmldlpdevnsllsakl'.
-
- From online servers, the results with a gap open penalty of 5 and gap
extend of 0.5 should be::
-
- https://www.ebi.ac.uk/Tools/psa/emboss_needle/
- EMBOSS_001
IHAAEEKDWKTAYSYb--g---FYEAFEGYdsidspk--aitslkymllckimlntpedvqalvsgkla
- :|||:|||.|||:||. | ||||||||||:|. |
|:|:||||||||:||:.|::|::|:|:||
- EMBOSS_001
LHAADEKDFKTAFSYabiggapFYEAFEGYdsvde-kvsaltalkymllckvmldlpdevnsllsakl-
-
- http://web.expasy.org/cgi-bin/sim/sim.pl?prot
- UserSeq1
IHAAEEKDWKTAYSYBG-----FYEAFEGYDSIDSPK--AITSLKYMLLCKIMLNTPEDVQALVSGKL
- UserSeq2
LHAADEKDFKTAFSYABIGGAPFYEAFEGYDSVDE-KVSALTALKYMLLCKVMLDLPDEVNSLLSAKL
- *** *** *** ** ********** * * * *
******** ** * * * * **
- """
-
- # The sequences.
- seq1 = 'IHAAEEKDWKTAYSYbgFYEAFEGYdsidspkaitslkymllckimlntpedvqalvsgkla'
- seq2 =
'LHAADEKDFKTAFSYabiggapFYEAFEGYdsvdekvsaltalkymllckvmldlpdevnsllsakl'
- print(seq1)
- print(seq2)
-
- # Perform the alignment.
- align1, align2, gaps = align_pairwise(seq1, seq2, matrix='PAM250',
gap_open_penalty=5.0, gap_extend_penalty=0.5)
- print(align1)
- print(align2)
- print(gaps)
-
- # Check the alignment.
- self.assertEqual(align1,
'IHAAEEKDWKTAYSYB--G---FYEAFEGYDSIDSPK--AITSLKYMLLCKIMLNTPEDVQALVSGKLA')
- self.assertEqual(align2,
'LHAADEKDFKTAFSYABIGGAPFYEAFEGYDSVDE-KVSALTALKYMLLCKVMLDLPDEVNSLLSAKL-')
-
- # The gap matrix.
- real_gaps = zeros((2, 69), int16)
- real_gaps[0, 16] = 1
- real_gaps[0, 17] = 1
- real_gaps[0, 19] = 1
- real_gaps[0, 20] = 1
- real_gaps[0, 21] = 1
- real_gaps[0, 37] = 1
- real_gaps[0, 38] = 1
- real_gaps[1, 35] = 1
- real_gaps[1, 68] = 1
- for i in range(2):
- for j in range(68):
- self.assertEqual(gaps[i, j], real_gaps[i][j])
def test_align_pairwise(self):
"""Test the Needleman-Wunsch sequence alignment for two protein
sequences.
@@ -109,7 +58,8 @@
print(seq2)
# Perform the alignment.
- align1, align2, gaps = align_pairwise(seq1, seq2, matrix='BLOSUM62',
gap_open_penalty=5.0, gap_extend_penalty=1.0)
+ score, align1, align2, gaps = align_pairwise(seq1, seq2,
matrix='BLOSUM62', gap_open_penalty=5.0, gap_extend_penalty=1.0)
+ print(score)
print(align1)
print(align2)
print(gaps)
@@ -160,7 +110,8 @@
print(seq2)
# Perform the alignment.
- align1, align2, gaps = align_pairwise(seq1, seq2, matrix='PAM250',
gap_open_penalty=5.0, gap_extend_penalty=0.5)
+ score, align1, align2, gaps = align_pairwise(seq1, seq2,
matrix='PAM250', gap_open_penalty=5.0, gap_extend_penalty=0.5)
+ print(score)
print(align1)
print(align2)
print(gaps)
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