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
