def test_score():
test_table = dp_table.DPTable("GCCCT", "GCGCA")
test_table.build_table()
test_table.base_cases()
test_table.fill_matrix()
test_table.get_score()
utils.print_table(test_table.table)
print(test_table.score)
def test_backtrack():
test_table = dp_table.DPTable("GCCCT", "GCGCA")
test_table.build_table()
test_table.base_cases()
test_table.fill_matrix()
utils.print_table(test_table.table)
test_table.backtrack()
print(test_table.aligned1)
print(test_table.aligned2)
def main():
seq_1, seq_2 = parse_args()
# Calculate and display Needleman-Wunsch
print('Needleman-Wunsch alignment:\n')
nw_table = dp_table.DPTable(seq_1, seq_2)
nw_table.calculate_alignment()
# utils.print_table(nw_table.table)
print('Score: {}'.format(nw_table.score))
utils.print_alignment(nw_table.aligned1, nw_table.aligned2)
# Calculate and display Smith-Waterman
print('\n\nSmith-Waterman alignment:\n')
sw_table = smith_waterman.SmithWaterman(seq_1, seq_2)
sw_table.calculate_alignment()
# utils.print_table(sw_table.table)
print('Score: {}'.format(sw_table.score))
print('Local alignment:')
utils.print_alignment(sw_table.alignment_1, sw_table.alignment_2)
def test_base_cases():
test_table = dp_table.DPTable("12345", "12345")
test_table.build_table()
test_table.base_cases()
utils.print_table(test_table.table)
def test_calc_value():
test_table = dp_table.DPTable("GCCCT", "GCGCA")
test_table.build_table()
test_table.base_cases()
test_table.fill_matrix()
utils.print_table(test_table.table)