def test_find_pattern_clumps_with_genome():
text = read_genome("genomics_algo/tests/test_data/e_coli.txt")
patterns = find_pattern_clumps(text=text,
substring_length=9,
window_length=500,
minimum_frequency=3)
assert len(patterns) == 1904
def test_get_occurences_with_exact_match_with_reverse_complement(
exact_matching_algo):
text = "GACTACGGAGACT"
pattern = "ACT"
result = get_occurences_with_exact_match_with_reverse_complement(
pattern, text, exact_matching_algo)
assert result == [1, 10]
text = "AAAAAAAAAACCCAAAAAAAAAAGGGAAAAAAAAAA"
pattern = "CCC"
result = get_occurences_with_exact_match_with_reverse_complement(
pattern, text, exact_matching_algo)
assert result == [10, 23]
text = "AAAAAAAAAACGCGAAAAAAAAAACGCGAAAAAAAAAA"
pattern = "CGCG"
result = get_occurences_with_exact_match_with_reverse_complement(
pattern, text, exact_matching_algo)
assert result == [10, 24]
text = read_genome("genomics_algo/tests/test_data/genomes/phix.fa")
pattern = "ATTA"
result = get_occurences_with_exact_match_with_reverse_complement(
pattern, text, exact_matching_algo)
assert min(result) == 62
assert len(result) == 60
def test_get_occurences_in_entire_genome_with_boyer_moores_exact_match(
exact_matching_algo, ):
text = read_genome(
"genomics_algo/tests/test_data/genomes/vibrio_cholerae.txt")
pattern = "ATGATCAAG"
result = exact_matching_algo(pattern, text)
assert result == [
116556,
149355,
151913,
152013,
152394,
186189,
194276,
200076,
224527,
307692,
479770,
610980,
653338,
679985,
768828,
878903,
985368,
]
def test_find_minimum_gc_skew_location_in_genome():
genome = read_genome("genomics_algo/tests/test_data/e_coli.txt")
result = find_minimum_gc_skew_location(genome)
np.testing.assert_array_equal([3923619, 3923620, 3923621, 3923622], result)
def test_read_genome():
genome = read_genome(
"genomics_algo/tests/test_data/genomes/lambda_virus.fa")
assert len(genome) == 48502
assert genome[:50] == "GGGCGGCGACCTCGCGGGTTTTCGCTATTTATGAAAATTTTCCGGTTTAA"