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#!/usr/bin/env python
from __future__ import division
from cogent.util.unit_test import TestCase, main
from cogent.align.algorithm import ScoreCell, MatchScorer, equality_scorer,\
default_gap, default_gap_symbol, ScoreMatrix, NeedlemanWunschMatrix, \
SmithWatermanMatrix, nw_align, sw_align
from copy import copy, deepcopy
__author__ = "Jeremy Widmann"
__copyright__ = "Copyright 2007-2009, The Cogent Project"
__credits__ = ["Jeremy Widmann", "Rob Knight"]
__license__ = "GPL"
__version__ = "1.4.1"
__maintainer__ = "Jeremy Widmann"
__email__ = "jeremy.widmann@colorado.edu"
__status__ = "Production"
"""Tests of the cogent.align.algorithm module.
"""
class ScoreCellTests(TestCase):
"""Tests for ScoreCell class.
"""
def setUp(self):
"""Setup for ScoreCell tests."""
self.score_cell = ScoreCell()
def test_init(self):
"""Tests for ScoreCell __init__ function."""
#Test for empty score cell
self.assertEqual(self.score_cell.Score,0)
self.assertEqual(self.score_cell.Pointer,None)
def test_update(self):
"""Tests for ScoreCell update function."""
#Test tie up wins
self.score_cell.update(1,1,1)
self.assertEqual(self.score_cell.Score,1)
self.assertEqual(self.score_cell.Pointer,"up")
#Test tie diag wins
self.score_cell.update(3,1,3)
self.assertEqual(self.score_cell.Score,3)
self.assertEqual(self.score_cell.Pointer,"diag")
#Test up
self.score_cell.update(1,1,1)
self.assertEqual(self.score_cell.Score,1)
self.assertEqual(self.score_cell.Pointer,"up")
#Test diag
self.score_cell.update(3,1,2)
self.assertEqual(self.score_cell.Score,3)
self.assertEqual(self.score_cell.Pointer,"diag")
#Test left
self.score_cell.update(1,2,3)
self.assertEqual(self.score_cell.Score,3)
self.assertEqual(self.score_cell.Pointer,"left")
class MatchScorerTests(TestCase):
"""Tests for MatchScorer function.
"""
def setUp(self):
"""Setup for MatchScorer tests."""
self.equality_scorer = MatchScorer(1,-1)
self.mismatch_worse_scorer = MatchScorer(1,-2)
self.match_worse_scorer = MatchScorer(-1,1)
def test_scorer(self):
"""Tests for MatchScorer function."""
#Test equality_scorer
self.assertEqual(self.equality_scorer('A','A'),1)
self.assertEqual(self.equality_scorer('A','B'),-1)
#Test mismatch_worse_scorer
self.assertEqual(self.mismatch_worse_scorer('A','A'),1)
self.assertEqual(self.mismatch_worse_scorer('A','B'),-2)
#Test match_worse_scorer
self.assertEqual(self.match_worse_scorer('A','A'),-1)
self.assertEqual(self.match_worse_scorer('A','B'),1)
class ScoreMatrixTests(TestCase):
"""Tests for ScoreCell class.
"""
def setUp(self):
"""Setup for ScoreMatrix tests."""
self.score_matrix = ScoreMatrix('AACGU','ACAGU')
def fill():
pass
def traceback():
pass
self.score_matrix.fill = fill
self.score_matrix.traceback = traceback
self.empty_score_matrix = ScoreMatrix('','')
def test_init(self):
"""Tests for ScoreMatrix __init__ function."""
#Test empty ScoreMatrix
self.empty_score_matrix = ScoreMatrix('','')
self.assertEqual(self.empty_score_matrix.First,'')
self.assertEqual(self.empty_score_matrix.Second,'')
self.assertEqual(self.empty_score_matrix.Cols,1)
self.assertEqual(self.empty_score_matrix.Rows,1)
self.assertEqual(self.empty_score_matrix.GapScore,-1)
self.assertEqual(self.empty_score_matrix.GapSymbol,'-')
self.assertEqual(self.empty_score_matrix.FirstAlign,[])
self.assertEqual(self.empty_score_matrix.SecondAlign,[])
def test_str(self):
"""Tests for ScoreMatrix __str__ function."""
#Test empty ScoreMatrix
self.assertEqual(self.empty_score_matrix.__str__(),"Empty Score Matrix")
#Test full ScoreMatrix
self.assertEqual(self.score_matrix.__str__(),\
"""\t\tA\tA\tC\tG\tU\n\t0\t0\t0\t0\t0\t0\nA\t0\t0\t0\t0\t0\t0\nC\t0\t0\t0\t0\t0\t0\nA\t0\t0\t0\t0\t0\t0\nG\t0\t0\t0\t0\t0\t0\nU\t0\t0\t0\t0\t0\t0""")
def test_alignment(self):
"""Tests for ScoreMatrix alignment function."""
#Should not align since ScoreMatrix base object does not have fill()
#or traceback() methods. For testing purposes fill() and traceback()
#for self.score_matrix do nothing.
self.assertEqual(self.score_matrix.alignment(),('',''))
class NeedlemanWunschMatrixTests(TestCase):
"""Tests for NeedlemanWunschMatrix class.
"""
def setUp(self):
"""Setup for NeedlemanWunschMatrix tests."""
self.nw_matrix = NeedlemanWunschMatrix('ACGU','CAGU')
#Since _init_first_row, _init_first_col and _init_first_cell are
#automatically called when NeedlemanWunschMatrix is initialized,
#need to change all elements in nw_matrix_empty to 0 to test
#that each _init works.
self.nw_matrix_empty = \
NeedlemanWunschMatrix('ACGU','CAGU')
for i in range(len(self.nw_matrix_empty)):
for j in range(len(self.nw_matrix_empty[i])):
self.nw_matrix_empty[i][j]=ScoreCell(0)
def test_init_first_row(self):
"""Tests for NeedlemanWunschMatrix _init_first_row function."""
nw_matrix_empty = copy(self.nw_matrix_empty)
#Init first row
nw_matrix_empty._init_first_row()
#matrix after first row init
matrix_scores_first_row_init = [[0,-1,-2,-3,-4],
[0,0,0,0,0],
[0,0,0,0,0],
[0,0,0,0,0],
[0,0,0,0,0]]
for i in range(len(nw_matrix_empty)):
for j in range(len(nw_matrix_empty[i])):
self.assertEqual(nw_matrix_empty[i][j].Score,\
matrix_scores_first_row_init[i][j])
def test_init_first_col(self):
"""Tests for NeedlemanWunschMatrix _init_first_col function."""
nw_matrix_empty = copy(self.nw_matrix_empty)
#Init first row
nw_matrix_empty._init_first_col()
#matrix after first row init
matrix_scores_first_row_init = [[0,0,0,0,0],
[-1,0,0,0,0],
[-2,0,0,0,0],
[-3,0,0,0,0],
[-4,0,0,0,0]]
for i in range(len(nw_matrix_empty)):
for j in range(len(nw_matrix_empty[i])):
self.assertEqual(nw_matrix_empty[i][j].Score,\
matrix_scores_first_row_init[i][j])
def test_init_first_cell(self):
"""Tests for NeedlemanWunschMatrix _init_first_cell function."""
nw_matrix_empty = copy(self.nw_matrix_empty)
#Init first row
nw_matrix_empty._init_first_cell()
self.assertEqual(nw_matrix_empty[0][0].Score,0)
def test_initialized_matrix(self):
"""Tests for NeedlemanWunschMatrix after full initialization."""
matrix_scores_first_row_init = [[0,-1,-2,-3,-4],
[-1,0,0,0,0],
[-2,0,0,0,0],
[-3,0,0,0,0],
[-4,0,0,0,0]]
for i in range(len(self.nw_matrix)):
for j in range(len(self.nw_matrix[i])):
self.assertEqual(self.nw_matrix[i][j].Score,\
matrix_scores_first_row_init[i][j])
def test_fill(self):
"""Tests for NeedlemanWunschMatrix fill function."""
filled_nw_matrix = copy(self.nw_matrix)
filled_nw_matrix.fill()
matrix_scores_filled = [[0,-1,-2,-3,-4],
[-1,-1,0,-1,-2],
[-2,0,-1,-1,-2],
[-3,-1,-1,0,-1],
[-4,-2,-2,-1,1]]
matrix_pointers_filled = [[None,'left','left','left','left'],
['up','diag','diag','left','left'],
['up','diag','up','diag','diag'],
['up','up','diag','diag','left'],
['up','up','up','up','diag']]
self.assertEqual(filled_nw_matrix.Filled,True)
for i in range(len(filled_nw_matrix)):
for j in range(len(filled_nw_matrix[i])):
self.assertEqual(filled_nw_matrix[i][j].Score,\
matrix_scores_filled[i][j])
self.assertEqual(filled_nw_matrix[i][j].Pointer,\
matrix_pointers_filled[i][j])
self.assertEqual(filled_nw_matrix.MaxScore,(1,4,4))
def test_traceback(self):
"""Tests for NeedlemanWunschMatrix traceback function."""
self.nw_matrix.traceback()
self.assertEqual(self.nw_matrix.FirstAlign,['A','C','-','G','U'])
self.assertEqual(self.nw_matrix.SecondAlign,['-','C','A','G','U'])
class SmithWatermanMatrixTests(TestCase):
"""Tests for SmithWatermanMatrix class.
"""
def setUp(self):
"""Setup for SmithWatermanMatrix tests."""
self.sw_matrix = SmithWatermanMatrix('ACGU','CAGU')
def test_fill(self):
"""Tests for SmithWatermanMatrix fill function."""
filled_sw_matrix = copy(self.sw_matrix)
filled_sw_matrix.fill()
matrix_scores_filled = [[0,0,0,0,0],
[0,0,1,0,0],
[0,1,0,0,0],
[0,0,0,1,0],
[0,0,0,0,2]]
matrix_pointers_filled = [[None,None,None,None,None],
[None,None,'diag',None,None],
[None,'diag',None,None,None],
[None,None,None,'diag',None],
[None,None,None,None,'diag']]
for i in range(len(filled_sw_matrix)):
for j in range(len(filled_sw_matrix[i])):
self.assertEqual(filled_sw_matrix[i][j].Score,\
matrix_scores_filled[i][j])
self.assertEqual(filled_sw_matrix[i][j].Pointer,\
matrix_pointers_filled[i][j])
self.assertEqual(filled_sw_matrix.MaxScore,(2,4,4))
def test_traceback(self):
"""Tests for SmithWatermanMatrix traceback function."""
self.sw_matrix.fill()
self.sw_matrix.traceback()
self.assertEqual(self.sw_matrix.FirstAlign,['G','U'])
self.assertEqual(self.sw_matrix.SecondAlign,['G','U'])
class NwAlignTests(TestCase):
"""Tests for nw_align fuction.
"""
def test_nw_align_empty(self):
"""Tests for nw_align function."""
(first,second),score = nw_align('','',return_score=True)
self.assertEqual(first,'')
self.assertEqual(second,'')
self.assertEqual(score,0)
def test_nw_align(self):
"""Tests for nw_align function."""
(first,second),score = nw_align('ACGU','CAGU',return_score=True)
self.assertEqual(first,'AC-GU')
self.assertEqual(second,'-CAGU')
self.assertEqual(score,1)
class SwAlignTests(TestCase):
"""Tests for sw_align function.
"""
def test_sw_align_empty(self):
"""Tests for sw_align function."""
(first,second),score = sw_align('','',return_score=True)
self.assertEqual(first,'')
self.assertEqual(second,'')
self.assertEqual(score,0)
def test_sw_align(self):
"""Tests for sw_align function."""
(first,second),score = sw_align('ACGU','CAGU',return_score=True)
self.assertEqual(first,'GU')
self.assertEqual(second,'GU')
self.assertEqual(score,2)
#run if called from command-line
if __name__ == "__main__":
main()
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