def test_dna_count_nucleotides_format(self):
expected = '20 12 17 21'
dna = DNA(
'AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC'
)
result = dna_count_nucleotides.format_string(dna)
assert expected == result
def test_count_nucleotides_success(self):
expected = {'A': 2, 'C': 1, 'G': 0, 'T': 3}
dna = DNA('ACTTAT')
result = dna.nucleotide_counts()
assert expected == result
def test_count_nucleotides_empty(self):
expected = {'A': 0, 'C': 0, 'G': 0, 'T': 0}
dna = DNA('')
result = dna.nucleotide_counts()
assert expected == result
def test_create_dna_success(self):
dna = DNA('ACGT')
assert dna.string == 'ACGT'
def main():
with open(get_rosalind_data_path('hamm')) as file:
dna = DNA(file.readline())
dna2 = DNA(file.readline())
print(dna.get_hamming_distance(dna2))
def test_polynucleotides_different_type(self):
dna = DNA("ACG")
rna = RNA("ACG")
assert dna != rna
def test_hamming_distance_diff(self):
expected = 7
dna = DNA("GAGCCTACTAACGGGAT")
dna2 = DNA("CATCGTAATGACGGCCT")
result = dna.get_hamming_distance(dna2)
assert expected == result
def test_dna_gc_content_success(self):
expected = 66.666
dna = DNA("CCGGTA")
result = dna.gc_content()
assert abs(expected - result) < 0.001
def test_dna_to_rna_success(self):
expected = RNA('ACGU')
dna = DNA('ACGT')
result = dna.to_rna()
assert expected == result
def test_count_nucleotides_success(self):
expected = {'A': 2, 'C': 1, 'G': 0, 'T': 3}
dna = DNA('ACTTAT')
result = dna.nucleotide_counts()
assert expected == result
def test_count_nucleotides_empty(self):
expected = {'A': 0, 'C': 0, 'G': 0, 'T': 0}
dna = DNA('')
result = dna.nucleotide_counts()
assert expected == result
def test_recv_dna_strand_complement_format(self):
expected = 'ACCGGGTTTT'
dna = DNA('AAAACCCGGT')
result = recv_dna_strand_complement.format_string(dna)
assert expected == result
def test_rna_dna_transcription_format(self):
expected = 'GAUGGAACUUGACUACGUAAAUU'
dna = DNA('GATGGAACTTGACTACGTAAATT')
result = rna_dna_transcription.format_string(dna)
assert expected == result
def main():
with open(get_rosalind_data_path('hamm')) as file:
dna = DNA(file.readline())
dna2 = DNA(file.readline())
print(dna.get_hamming_distance(dna2))
def test_dna_to_rna_success(self):
expected = RNA('ACGU')
dna = DNA('ACGT')
result = dna.to_rna()
assert expected == result
def test_dna_reverse_complement_success(self):
expected = 'CGTA'
dna = DNA('TACG')
result = dna.reverse_complement()
assert result == expected
def test_dna_reverse_complement_success(self):
expected = 'CGTA'
dna = DNA('TACG')
result = dna.reverse_complement()
assert result == expected
def test_dna_gc_content_success(self):
expected = 66.666
dna = DNA("CCGGTA")
result = dna.gc_content()
assert abs(expected-result) < 0.001
def test_hamming_distance_no_diff(self):
expected = 0
dna = DNA("CCC")
dna2 = DNA("CCC")
result = dna.get_hamming_distance(dna2)
assert expected == result
def test_hamming_distance_no_diff(self):
expected = 0
dna = DNA("CCC")
dna2 = DNA("CCC")
result = dna.get_hamming_distance(dna2)
assert expected == result
def test_create_dna_wrong_values(self):
with pytest.raises(ValueError) as ve_info:
DNA('AUGCT')
def test_hamming_distance_diff(self):
expected = 7
dna = DNA("GAGCCTACTAACGGGAT")
dna2 = DNA("CATCGTAATGACGGCCT")
result = dna.get_hamming_distance(dna2)
assert expected == result
def main():
with open(get_rosalind_data_path('rna')) as file:
dna = DNA(file.read())
print(format_string(dna))
def main():
with open(get_rosalind_data_path('subs')) as file:
DNAs = DNA(file.readline())
DNAt = DNA(file.readline())
index_list = map(lambda x: x, DNAs.find_substring_locations(DNAt))
print(format_string(index_list))