def test_compute_local_alignment(): """ Test the function compute_global_alignment function """ suite = poc_simpletest.TestSuite() scoring_matrix = proj4_solution.build_scoring_matrix(set(["A", "C", "T", "G"]), 10, 4, -6) alignment_matrix = proj4_solution.compute_alignment_matrix("AA", "TAAT", scoring_matrix, False) local_alignment_sequence = proj4_solution.compute_local_alignment("AA", "TAAT", scoring_matrix, alignment_matrix) print local_alignment_sequence suite.run_test(local_alignment_sequence, (20, "AA", "AA"), "Error Found") scoring_matrix = proj4_solution.build_scoring_matrix(set(["A", "C", "T", "G"]), 10, 2, -4) alignment_matrix = proj4_solution.compute_alignment_matrix("---AC-C--", "TTTACACGG", scoring_matrix, False) local_alignment_sequence = proj4_solution.compute_local_alignment( "---AC-C--", "TTTACACGG", scoring_matrix, alignment_matrix ) print local_alignment_sequence suite.run_test(local_alignment_sequence, (26, "AC-C", "ACAC"), "Error Found") local_alignment_sequence = proj4_solution.compute_local_alignment( "A", "A", { "A": {"A": 6, "C": 2, "-": -4, "T": 2, "G": 2}, "C": {"A": 2, "C": 6, "-": -4, "T": 2, "G": 2}, "-": {"A": -4, "C": -4, "-": -4, "T": -4, "G": -4}, "G": {"A": 2, "C": 2, "-": -4, "T": 2, "G": 6}, }, [[0, 0], [0, 6]], ) print local_alignment_sequence suite.run_test(local_alignment_sequence, (6, "A", "A"), "Error Found") suite.report_results()
def test_compute_local_alignment(): """ Test the function compute_global_alignment function """ suite = poc_simpletest.TestSuite() scoring_matrix = proj4_solution.build_scoring_matrix( set(['A', 'C', 'T', 'G']), 10, 4, -6) alignment_matrix = proj4_solution.compute_alignment_matrix( 'AA', 'TAAT', scoring_matrix, False) local_alignment_sequence = proj4_solution.compute_local_alignment( 'AA', 'TAAT', scoring_matrix, alignment_matrix) print local_alignment_sequence suite.run_test(local_alignment_sequence, (20, 'AA', 'AA'), "Error Found") scoring_matrix = proj4_solution.build_scoring_matrix( set(['A', 'C', 'T', 'G']), 10, 2, -4) alignment_matrix = proj4_solution.compute_alignment_matrix( '---AC-C--', 'TTTACACGG', scoring_matrix, False) local_alignment_sequence = proj4_solution.compute_local_alignment( '---AC-C--', 'TTTACACGG', scoring_matrix, alignment_matrix) print local_alignment_sequence suite.run_test(local_alignment_sequence, (26, 'AC-C', 'ACAC'), "Error Found") local_alignment_sequence = proj4_solution.compute_local_alignment( 'A', 'A', { 'A': { 'A': 6, 'C': 2, '-': -4, 'T': 2, 'G': 2 }, 'C': { 'A': 2, 'C': 6, '-': -4, 'T': 2, 'G': 2 }, '-': { 'A': -4, 'C': -4, '-': -4, 'T': -4, 'G': -4 }, 'G': { 'A': 2, 'C': 2, '-': -4, 'T': 2, 'G': 6 } }, [[0, 0], [0, 6]]) print local_alignment_sequence suite.run_test(local_alignment_sequence, (6, 'A', 'A'), "Error Found") suite.report_results()
def test_build_scoring_matrix(): """ Test the running of build_scoring_matrix function """ suite = poc_simpletest.TestSuite() alphabet = set("abcd") scoring_matrix = proj4_solution.build_scoring_matrix(alphabet, 10, 4, -4) print scoring_matrix suite.run_test(scoring_matrix["a"]["a"], 10, "Something is wrong") scoring_matrix = proj4_solution.build_scoring_matrix(set(["A", "C", "T", "G"]), 6, 2, -4) print scoring_matrix suite.run_test(scoring_matrix["A"]["A"], 6, "Something is wrong") suite.report_results()
def test_build_scoring_matrix(): """ Test the running of build_scoring_matrix function """ suite = poc_simpletest.TestSuite() alphabet = set("abcd") scoring_matrix = proj4_solution.build_scoring_matrix(alphabet, 10, 4, -4) print scoring_matrix suite.run_test(scoring_matrix['a']['a'], 10, 'Something is wrong') scoring_matrix = proj4_solution.build_scoring_matrix( set(['A', 'C', 'T', 'G']), 6, 2, -4) print scoring_matrix suite.run_test(scoring_matrix['A']['A'], 6, 'Something is wrong') suite.report_results()
def test_compute_global_alignment(): """ Test the function compute_global_alignment function """ suite = poc_simpletest.TestSuite() scoring_matrix = proj4_solution.build_scoring_matrix(set(["A", "C", "T", "G"]), 10, 4, -6) alignment_matrix = proj4_solution.compute_alignment_matrix("AA", "TAAT", scoring_matrix, True) global_alignment_sequence = proj4_solution.compute_global_alignment("AA", "TAAT", scoring_matrix, alignment_matrix) print global_alignment_sequence suite.run_test(global_alignment_sequence, (8, "-AA-", "TAAT"), "Error Found") global_alignment_sequence = proj4_solution.compute_global_alignment( "ACTACT", "AGCTA", { "A": {"A": 2, "C": 1, "-": 0, "T": 1, "G": 1}, "C": {"A": 1, "C": 2, "-": 0, "T": 1, "G": 1}, "-": {"A": 0, "C": 0, "-": 0, "T": 0, "G": 0}, "T": {"A": 1, "C": 1, "-": 0, "T": 2, "G": 1}, "G": {"A": 1, "C": 1, "-": 0, "T": 1, "G": 2}, }, [ [0, 0, 0, 0, 0, 0], [0, 2, 2, 2, 2, 2], [0, 2, 3, 4, 4, 4], [0, 2, 3, 4, 6, 6], [0, 2, 3, 4, 6, 8], [0, 2, 3, 5, 6, 8], [0, 2, 3, 5, 7, 8], ], ) print global_alignment_sequence suite.run_test(global_alignment_sequence, (8, "A-CTACT", "AGCTA--"), "Error Found") global_alignment_sequence = proj4_solution.compute_global_alignment( "ACTACT", "GGACTGCTTCTGG", { "A": {"A": 2, "C": 1, "-": 0, "T": 1, "G": 1}, "C": {"A": 1, "C": 2, "-": 0, "T": 1, "G": 1}, "-": {"A": 0, "C": 0, "-": 0, "T": 0, "G": 0}, "T": {"A": 1, "C": 1, "-": 0, "T": 2, "G": 1}, "G": {"A": 1, "C": 1, "-": 0, "T": 1, "G": 2}, }, [ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], [0, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4], [0, 1, 2, 3, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6], [0, 1, 2, 4, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7], [0, 1, 2, 4, 6, 6, 7, 9, 9, 9, 9, 9, 9, 9], [0, 1, 2, 4, 6, 8, 8, 9, 11, 11, 11, 11, 11, 11], ], ) print global_alignment_sequence suite.run_test(global_alignment_sequence, (11, "--A---CTACT--", "GGACTGCTTCTGG"), "Error Found") suite.report_results()
def test_compute_alignment_matrix(): """ Test the function compute_alignment_matrix function """ suite = poc_simpletest.TestSuite() scoring_matrix = proj4_solution.build_scoring_matrix(set(["A", "C", "T", "G"]), 10, 4, -6) global_alignment_matrix = proj4_solution.compute_alignment_matrix("AA", "TAAT", scoring_matrix, False) print global_alignment_matrix suite.run_test(global_alignment_matrix[1][2], 4, "Error Found") suite.report_results()
def test_compute_alignment_matrix(): """ Test the function compute_alignment_matrix function """ suite = poc_simpletest.TestSuite() scoring_matrix = proj4_solution.build_scoring_matrix( set(['A', 'C', 'T', 'G']), 10, 4, -6) global_alignment_matrix = proj4_solution.compute_alignment_matrix( 'AA', 'TAAT', scoring_matrix, False) print global_alignment_matrix suite.run_test(global_alignment_matrix[1][2], 4, "Error Found") suite.report_results()
def check_spelling(checked_word, dist, word_list): """ Helper function for Question: 8 :param checked_word: The target word :param dist: The given edit_distance :param word_list: The given list of words :return: A set of all words that are within the given edit_distance from the checked_word. """ outcome_set = set() scoring_matrix = student.build_scoring_matrix(lowercase, 2, 1, 0) len_checked_word = len(checked_word) for word in word_list: if abs(len(word) - len_checked_word <= dist): edit_distance = compute_edit_distance(word, checked_word, scoring_matrix) if edit_distance <= dist: outcome_set.add(word) return outcome_set
def test_compute_global_alignment(): """ Test the function compute_global_alignment function """ suite = poc_simpletest.TestSuite() scoring_matrix = proj4_solution.build_scoring_matrix( set(['A', 'C', 'T', 'G']), 10, 4, -6) alignment_matrix = proj4_solution.compute_alignment_matrix( 'AA', 'TAAT', scoring_matrix, True) global_alignment_sequence = proj4_solution.compute_global_alignment( 'AA', 'TAAT', scoring_matrix, alignment_matrix) print global_alignment_sequence suite.run_test(global_alignment_sequence, (8, '-AA-', 'TAAT'), "Error Found") global_alignment_sequence = proj4_solution.compute_global_alignment( 'ACTACT', 'AGCTA', { 'A': { 'A': 2, 'C': 1, '-': 0, 'T': 1, 'G': 1 }, 'C': { 'A': 1, 'C': 2, '-': 0, 'T': 1, 'G': 1 }, '-': { 'A': 0, 'C': 0, '-': 0, 'T': 0, 'G': 0 }, 'T': { 'A': 1, 'C': 1, '-': 0, 'T': 2, 'G': 1 }, 'G': { 'A': 1, 'C': 1, '-': 0, 'T': 1, 'G': 2 } }, [[0, 0, 0, 0, 0, 0], [0, 2, 2, 2, 2, 2], [0, 2, 3, 4, 4, 4], [0, 2, 3, 4, 6, 6], [0, 2, 3, 4, 6, 8], [0, 2, 3, 5, 6, 8], [0, 2, 3, 5, 7, 8]]) print global_alignment_sequence suite.run_test(global_alignment_sequence, (8, 'A-CTACT', 'AGCTA--'), "Error Found") global_alignment_sequence = proj4_solution.compute_global_alignment( 'ACTACT', 'GGACTGCTTCTGG', { 'A': { 'A': 2, 'C': 1, '-': 0, 'T': 1, 'G': 1 }, 'C': { 'A': 1, 'C': 2, '-': 0, 'T': 1, 'G': 1 }, '-': { 'A': 0, 'C': 0, '-': 0, 'T': 0, 'G': 0 }, 'T': { 'A': 1, 'C': 1, '-': 0, 'T': 2, 'G': 1 }, 'G': { 'A': 1, 'C': 1, '-': 0, 'T': 1, 'G': 2 } }, [[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2], [0, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4], [0, 1, 2, 3, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6], [0, 1, 2, 4, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7], [0, 1, 2, 4, 6, 6, 7, 9, 9, 9, 9, 9, 9, 9], [0, 1, 2, 4, 6, 8, 8, 9, 11, 11, 11, 11, 11, 11]]) print global_alignment_sequence suite.run_test(global_alignment_sequence, (11, '--A---CTACT--', 'GGACTGCTTCTGG'), "Error Found") suite.report_results()