def setUp(self):
aligner = PairwiseAligner()
aligner.internal_open_gap_score = -1
aligner.internal_extend_gap_score = -0.0
aligner.match_score = +1
aligner.mismatch_score = -1
aligner.mode = "local"
self.aligner = aligner
def perform_randomized_tests(n=1000):
"""Perform randomized tests and compare to pslMap.
Run this function to perform 8 x n mappings for alignments of randomly
generated sequences, get the alignment in PSL format, and compare the
result to that of pslMap.
"""
aligner = PairwiseAligner()
aligner.internal_open_gap_score = -1
aligner.internal_extend_gap_score = -0.0
aligner.match_score = +1
aligner.mismatch_score = -1
aligner.mode = "local"
for i in range(n):
nBlocks1 = random.randint(1, 10)
nBlocks2 = random.randint(1, 10)
test_random(aligner, nBlocks1, nBlocks2, "+", "+")
test_random(aligner, nBlocks1, nBlocks2, "+", "-")
test_random(aligner, nBlocks1, nBlocks2, "-", "+")
test_random(aligner, nBlocks1, nBlocks2, "-", "-")
test_random_sequences("+", "+")
test_random_sequences("+", "-")
test_random_sequences("-", "+")
test_random_sequences("-", "-")