Author: bugman
Date: Wed Jan 28 18:24:15 2015
New Revision: 27344
URL: http://svn.gna.org/viewcvs/relax?rev=27344&view=rev
Log:
Created the Test_align_protein.test_align_multiple_from_pairwise unit test.
This is in the _lib._sequence_alignment.test_align_protein unit test module.
This test checks the
operation of the
lib.sequence_alignment.align_protein.align_multiple_from_pairwise() function,
which
does not yet exist.
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=27344&r1=27343&r2=27344&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
Wed Jan 28 18:24:15 2015
@@ -24,60 +24,59 @@
from unittest import TestCase
# relax module imports.
-from lib.sequence_alignment.align_protein import align_pairwise
+from lib.sequence_alignment.align_protein import align_multiple_from_pairwise,
align_pairwise
class Test_align_protein(TestCase):
"""Unit tests for the lib.sequence_alignment.align_protein relax module."""
- def test_align_pairwise(self):
- """Test the Needleman-Wunsch sequence alignment for two protein
sequences.
-
- This uses the sequences:
-
- - 'IHAAEEKDWKTAYSYbgFYEAFEGYdsidspkaitslkymllckimlntpedvqalvsgkla',
- -
'LHAADEKDFKTAFSYabiggapFYEAFEGYdsvdekvsaltalkymllckvmldlpdevnsllsakl'.
-
- 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
IHAAEEKDWKTAYSY-B-G---FYEAFEGYDSIDSP-KAITSLKYMLLCKIMLNTPEDVQALVSGKLA
- :|||:|||:|||:|| | | ||||||||||:|..
.|:|:||||||||:||:.|::|.:|:|.||
- EMBOSS_001
LHAADEKDFKTAFSYABIGGAPFYEAFEGYDSVDEKVSALTALKYMLLCKVMLDLPDEVNSLLSAKL-
-
- http://web.expasy.org/cgi-bin/sim/sim.pl?prot
- UserSeq1
IHAAEEKDWKTAYSY-B-G---FYEAFEGYDSIDSP-KAITSLKYMLLCKIMLNTPEDVQALVSGKL
- UserSeq2
LHAADEKDFKTAFSYABIGGAPFYEAFEGYDSVDEKVSALTALKYMLLCKVMLDLPDEVNSLLSAKL
- *** *** *** ** * * ********** * * *
******** ** * * * * **
- """
-
- # The sequences.
- seq1 = 'IHAAEEKDWKTAYSYbgFYEAFEGYdsidspkaitslkymllckimlntpedvqalvsgkla'
- seq2 =
'LHAADEKDFKTAFSYabiggapFYEAFEGYdsvdekvsaltalkymllckvmldlpdevnsllsakl'
- print(seq1)
- print(seq2)
-
- # Perform the alignment.
- align1, align2, gaps = align_pairwise(seq1, seq2, matrix='BLOSUM62',
gap_open_penalty=5.0, gap_extend_penalty=1.0)
- print(align1)
- print(align2)
- print(gaps)
-
- # Check the alignment.
- self.assertEqual(align1,
'IHAAEEKDWKTAYSY-B-G---FYEAFEGYDSIDSP-KAITSLKYMLLCKIMLNTPEDVQALVSGKLA')
- self.assertEqual(align2,
'LHAADEKDFKTAFSYABIGGAPFYEAFEGYDSVDEKVSALTALKYMLLCKVMLDLPDEVNSLLSAKL-')
-
- # The gap matrix.
- real_gaps = zeros((2, 68), int16)
- real_gaps[0, 15] = 1
- real_gaps[0, 17] = 1
- real_gaps[0, 19] = 1
- real_gaps[0, 20] = 1
- real_gaps[0, 21] = 1
- real_gaps[0, 36] = 1
- real_gaps[1, 67] = 1
- for i in range(2):
- for j in range(68):
+ def test_align_multiple_from_pairwise(self):
+ """Test the multiple protein sequence, fusing pairwise alignments via
lib.sequence_alignment.align_protein.align_multiple_from_pairwise().
+
+ This uses the sequences:
+
+ - 'TEEQVDADGGT',
+ - 'ADQLTEEQVDADGNGTIDFPEFLTMMARKM',
+ - 'LTEEQMINEVDAGNGTIDFPEFLTMMAR'.
+
+ The result should be:
+
+ - '----TEEQ----VDADG-GT--------------',
+ - 'ADQLTEEQ----VDADGNGTIDFPEFLTMMARKM',
+ - '
+---LTEEQMINEVDA-GNGTIDFPEFLTMMAR--'.
+ """
+
+ # The sequences.
+ seq1 = 'TEEQVDADGGT'
+ seq2 = 'ADQLTEEQVDADGNGTIDFPEFLTMMARKM'
+ seq3 = 'LTEEQMINEVDAGNGTIDFPEFLTMMAR'
+ print(seq1)
+ print(seq2)
+ print(seq3)
+
+ # Perform the alignment.
+ strings, gaps = align_multiple_from_pairwise(seq1, [seq2, seq3],
matrix='BLOSUM62', gap_open_penalty=5.0, gap_extend_penalty=1.0)
+ print(strings[0])
+ print(strings[1])
+ print(strings[2])
+ print(gaps)
+
+ # Check the alignment.
+ self.assertEqual(strings[0], '----TEEQ----VDADG-GT--------------')
+ self.assertEqual(strings[1], 'ADQLTEEQ----VDADGNGTIDFPEFLTMMARKM')
+ self.assertEqual(strings[2], '---LTEEQMINEVDA-GNGTIDFPEFLTMMAR--')
+
+ # The gap matrix.
+ real_gaps = zeros((3, 34), int16)
+ for i in (range(4) + range(8, 12) + [17] + range(20, 34)):
+ real_gaps[0, i] = 1
+ for i in range(8, 12):
+ real_gaps[1, i] = 1
+ for i in (range(3) + [15, 33, 34]):
+ real_gaps[2, i] = 1
+ for i in range(3):
+ for j in range(34):
self.assertEqual(gaps[i, j], real_gaps[i][j])
@@ -132,3 +131,105 @@
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.
+
+ This uses the sequences:
+
+ - 'IHAAEEKDWKTAYSYbgFYEAFEGYdsidspkaitslkymllckimlntpedvqalvsgkla',
+ -
'LHAADEKDFKTAFSYabiggapFYEAFEGYdsvdekvsaltalkymllckvmldlpdevnsllsakl'.
+
+ 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
IHAAEEKDWKTAYSY-B-G---FYEAFEGYDSIDSP-KAITSLKYMLLCKIMLNTPEDVQALVSGKLA
+ :|||:|||:|||:|| | | ||||||||||:|..
.|:|:||||||||:||:.|::|.:|:|.||
+ EMBOSS_001
LHAADEKDFKTAFSYABIGGAPFYEAFEGYDSVDEKVSALTALKYMLLCKVMLDLPDEVNSLLSAKL-
+
+ http://web.expasy.org/cgi-bin/sim/sim.pl?prot
+ UserSeq1
IHAAEEKDWKTAYSY-B-G---FYEAFEGYDSIDSP-KAITSLKYMLLCKIMLNTPEDVQALVSGKL
+ UserSeq2
LHAADEKDFKTAFSYABIGGAPFYEAFEGYDSVDEKVSALTALKYMLLCKVMLDLPDEVNSLLSAKL
+ *** *** *** ** * * ********** * * *
******** ** * * * * **
+ """
+
+ # The sequences.
+ seq1 = 'IHAAEEKDWKTAYSYbgFYEAFEGYdsidspkaitslkymllckimlntpedvqalvsgkla'
+ seq2 =
'LHAADEKDFKTAFSYabiggapFYEAFEGYdsvdekvsaltalkymllckvmldlpdevnsllsakl'
+ print(seq1)
+ print(seq2)
+
+ # Perform the alignment.
+ align1, align2, gaps = align_pairwise(seq1, seq2, matrix='BLOSUM62',
gap_open_penalty=5.0, gap_extend_penalty=1.0)
+ print(align1)
+ print(align2)
+ print(gaps)
+
+ # Check the alignment.
+ self.assertEqual(align1,
'IHAAEEKDWKTAYSY-B-G---FYEAFEGYDSIDSP-KAITSLKYMLLCKIMLNTPEDVQALVSGKLA')
+ self.assertEqual(align2,
'LHAADEKDFKTAFSYABIGGAPFYEAFEGYDSVDEKVSALTALKYMLLCKVMLDLPDEVNSLLSAKL-')
+
+ # The gap matrix.
+ real_gaps = zeros((2, 68), int16)
+ real_gaps[0, 15] = 1
+ real_gaps[0, 17] = 1
+ real_gaps[0, 19] = 1
+ real_gaps[0, 20] = 1
+ real_gaps[0, 21] = 1
+ real_gaps[0, 36] = 1
+ real_gaps[1, 67] = 1
+ for i in range(2):
+ for j in range(68):
+ self.assertEqual(gaps[i, j], real_gaps[i][j])
+
+
+ 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])
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