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 local_alignment_eyeless_protein(): """ Question: 1 """ human_eyeless_seq = provided.read_protein(provided.HUMAN_EYELESS_URL) fruitfly_eyeless_seq = provided.read_protein(provided.FRUITFLY_EYELESS_URL) scoring_matrix = provided.read_scoring_matrix(provided.PAM50_URL) alignment_matrix = student.compute_alignment_matrix(human_eyeless_seq, fruitfly_eyeless_seq, scoring_matrix, False) local_alignment = student.compute_local_alignment(human_eyeless_seq, fruitfly_eyeless_seq, scoring_matrix, alignment_matrix) return local_alignment
def local_alignment_eyeless_protein(): """ Question: 1 """ human_eyeless_seq = provided.read_protein(provided.HUMAN_EYELESS_URL) fruitfly_eyeless_seq = provided.read_protein(provided.FRUITFLY_EYELESS_URL) scoring_matrix = provided.read_scoring_matrix(provided.PAM50_URL) alignment_matrix = student.compute_alignment_matrix( human_eyeless_seq, fruitfly_eyeless_seq, scoring_matrix, False) local_alignment = student.compute_local_alignment(human_eyeless_seq, fruitfly_eyeless_seq, scoring_matrix, alignment_matrix) return local_alignment