def test1(self):
# x x x c d e
filled_matrix = [
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0], # a
[0, 0, 0, 0, 0, 0, 0], # b
[0, 0, 0, 0, 2, 1, 0], # c
[0, 2, 2, 2, 1, 1, 0], # x
[0, 1, 1, 1, 1, 3, 2], # d
[0, 0, 0, 0, 0, 2, 5], # e
[0, 2, 2, 2, 1, 1, 4]
] # x
list1 = "abcxdex"
list2 = "xxxcde"
alignment = SmithWaterman.do_alignment(list1, list2, filled_matrix)
self.assertEqual(
alignment,
[['c', 'x', 'd', 'e'], ['|', ' ', '|', '|'], ['c', '-', 'd', 'e']])
def test2(self):
# T A C G G G T A T
filled_matrix = [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 1, 1, 1, 0, 0, 0], # G
[0, 0, 0, 0, 1, 2, 2, 1, 0, 0], # G
[0, 0, 1, 0, 0, 1, 1, 1, 2, 1], # A
[0, 0, 0, 2, 1, 0, 0, 0, 1, 1], # C
[0, 0, 0, 1, 3, 2, 1, 0, 0, 0], # G
[0, 1, 0, 0, 2, 2, 1, 2, 1, 1], # T
[0, 0, 2, 1, 1, 1, 1, 1, 3, 2], # A
[0, 0, 1, 3, 2, 1, 0, 0, 2, 2], # C
[0, 0, 0, 2, 4, 3, 2, 1, 1, 1]
] # G
list1 = "GGACGTACG"
list2 = "TACGGGTAT"
alignment = SmithWaterman.do_alignment(list1, list2, filled_matrix)
self.assertEqual(
alignment,
[['T', 'A', 'C', 'G'], ['|', '|', '|', '|'], ['T', 'A', 'C', 'G']])
def test3(self):
# G G A C A A A C G
filled_matrix = [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 1, 1, 0, 0, 0, 0, 0, 0, 0], # G
[0, 1, 2, 1, 0, 0, 0, 0, 0, 1], # G
[0, 0, 1, 3, 2, 1, 1, 1, 0, 0], # A
[0, 0, 0, 2, 4, 3, 2, 1, 1, 0], # C
[0, 1, 1, 1, 3, 3, 2, 1, 0, 1], # G
[0, 0, 0, 0, 2, 2, 2, 1, 0, 0], # T
[0, 0, 0, 1, 1, 3, 3, 3, 2, 1], # A
[0, 0, 0, 0, 1, 2, 2, 2, 4, 3], # C
[0, 1, 1, 0, 0, 1, 1, 1, 3, 5]
] # G
list1 = "GGACGTACG"
list2 = "GGACAAACG"
alignment = SmithWaterman.do_alignment(list1, list2, filled_matrix)
self.assertEqual(alignment,
[['G', 'G', 'A', 'C', 'G', 'T', 'A', 'C', 'G'],
['|', '|', '|', '|', '.', '.', '|', '|', '|'],
['G', 'G', 'A', 'C', 'A', 'A', 'A', 'C', 'G']])
import SmithWaterman
import AlignmentTools
file1 = SmithWaterman.get_file_data("Enter first file name: ")
file2 = SmithWaterman.get_file_data("Enter second file name: ")
file1list = list(file1)
file2list = list(file2)
file1len = len(file1list)
file2len = len(file2list)
matrix = SmithWaterman.create_matrix(file1len, file2len)
AlignmentTools.fill_matrix(file1list, file2list, matrix)
alignment = SmithWaterman.do_alignment(file1list, file2list, matrix)
print(''.join(alignment[0]))
print(''.join(alignment[1]))
print(''.join(alignment[2]))
