Source Code for Module test_suite.unit_tests._lib._sequence_alignment.test_msa

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2015 Edward d'Auvergne                                        # 
  4  #                                                                             # 
  5  # This file is part of the program relax (http://www.nmr-relax.com).          # 
  6  #                                                                             # 
  7  # This program is free software: you can redistribute it and/or modify        # 
  8  # it under the terms of the GNU General Public License as published by        # 
  9  # the Free Software Foundation, either version 3 of the License, or           # 
 10  # (at your option) any later version.                                         # 
 11  #                                                                             # 
 12  # This program is distributed in the hope that it will be useful,             # 
 13  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
 14  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               # 
 15  # GNU General Public License for more details.                                # 
 16  #                                                                             # 
 17  # You should have received a copy of the GNU General Public License           # 
 18  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
 19  #                                                                             # 
 20  ############################################################################### 
 21   
 22  # Python module imports. 
 23  from numpy import int16, zeros 
 24  from unittest import TestCase 
 25   
 26  # relax module imports. 
 27  from lib.sequence_alignment.msa import central_star 
 28   
 29   
 30 -class Test_msa(TestCase): 
 31      """Unit tests for the lib.sequence_alignment.msa relax module.""" 
 32   
 33 -    def test_central_star(self): 
 34          """Test the central star multiple sequence alignment function lib.sequence_alignment.msa.central_star(). 
 35   
 36          This uses the sequences: 
 37   
 38              - 'TEEQVDADGGT', 
 39              - 'ADQLTEEQVDADGNGTIDFPEFLTMMARKM', 
 40              - 'LTEEQMINEVDAGNGTIDFPEFLTMMAR'. 
 41   
 42          The result should be:: 
 43   
 44              Pairwise protein alignment. 
 45              Substitution matrix:           BLOSUM62 
 46              Gap opening penalty:           5.0 
 47              Gap extend penalty:            1.0 
 48               
 49              Input sequence 1:              TEEQVDADGGT 
 50              Input sequence 2:              ADQLTEEQVDADGNGTIDFPEFLTMMARKM 
 51               
 52              Aligned sequence 1:            ----TEEQVDADG-GT-------------- 
 53              Aligned sequence 2:            ADQLTEEQVDADGNGTIDFPEFLTMMARKM 
 54                                                 ********* **               
 55               
 56               
 57              Pairwise protein alignment. 
 58              Substitution matrix:           BLOSUM62 
 59              Gap opening penalty:           5.0 
 60              Gap extend penalty:            1.0 
 61               
 62              Input sequence 1:              TEEQVDADGGT 
 63              Input sequence 2:              LTEEQMINEVDAGNGTIDFPEFLTMMAR 
 64               
 65              Aligned sequence 1:            -TEEQ----VDADGGT------------ 
 66              Aligned sequence 2:            LTEEQMINEVDAGNGTIDFPEFLTMMAR 
 67                                              ****    ***  **             
 68   
 69              ----TEEQ----VDADG-GT-------------- 
 70              ADQLTEEQ----VDADGNGTIDFPEFLTMMARKM 
 71              ---LTEEQMINEVDA-GNGTIDFPEFLTMMAR-- 
 72          """ 
 73   
 74          # The sequences. 
 75          seq1 =     'TEEQVDADGGT' 
 76          seq2 = 'ADQLTEEQVDADGNGTIDFPEFLTMMARKM' 
 77          seq3 =    'LTEEQMINEVDAGNGTIDFPEFLTMMAR' 
 78   
 79          # Perform the alignment. 
 80          strings, gaps = central_star([seq1, seq2, seq3], matrix='BLOSUM62', gap_open_penalty=5.0, gap_extend_penalty=1.0) 
 81          print(strings[0]) 
 82          print(strings[1]) 
 83          print(strings[2]) 
 84          print(gaps) 
 85   
 86          # Check the alignment. 
 87          self.assertEqual(strings[0], '----TEEQ----VDADG-GT--------------') 
 88          self.assertEqual(strings[1], 'ADQLTEEQ----VDADGNGTIDFPEFLTMMARKM') 
 89          self.assertEqual(strings[2], '---LTEEQMINEVDA-GNGTIDFPEFLTMMAR--') 
 90   
 91          # The gap matrix. 
 92          real_gaps = zeros((3, 34), int16) 
 93          for i in (list(range(4)) + list(range(8, 12)) + [17] + list(range(20, 34))): 
 94              real_gaps[0, i] = 1 
 95          for i in range(8, 12): 
 96              real_gaps[1, i] = 1 
 97          for i in (list(range(3)) + [15, 32, 33]): 
 98              real_gaps[2, i] = 1 
 99          for i in range(3): 
100              for j in range(34): 
101                  self.assertEqual(gaps[i, j], real_gaps[i][j]) 
102