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from sqt.dna import (reverse_complement, n_intervals, intervals_complement,
amino_acid_regex, GENETIC_CODE, nt_to_aa)
def test_complement_string():
rc = reverse_complement
assert rc('') == ''
assert rc('A') == 'T'
assert rc('C') == 'G'
assert rc('TG') == 'CA'
assert rc('N') == 'N'
assert rc('a') == 't'
assert rc('ACGTUMRWSYKVHDBN') == 'NVHDBMRSWYKAACGT'
assert rc('acgtumrwsykvhdbn') == 'nvhdbmrswykaacgt'
assert rc('ACGTUMRWSYKVHDBNacgtumrwsykvhdbn') == 'nvhdbmrswykaacgtNVHDBMRSWYKAACGT'
#ACGTUMRWSYKVHDBN
#TGCAAKYWSRMBDHVN
def test_complement_bytes():
rc = reverse_complement
assert rc(b'') == b''
assert rc(b'A') == b'T'
assert rc(b'C') == b'G'
assert rc(b'TG') == b'CA'
assert rc(b'N') == b'N'
assert rc(b'a') == b't'
assert rc(b'ACGTUMRWSYKVHDBN') == b'NVHDBMRSWYKAACGT'
assert rc(b'acgtumrwsykvhdbn') == b'nvhdbmrswykaacgt'
assert rc(b'ACGTUMRWSYKVHDBNacgtumrwsykvhdbn') == b'nvhdbmrswykaacgtNVHDBMRSWYKAACGT'
def test_n_intervals():
assert list(n_intervals(b'', N=ord(b'N'))) == []
assert list(n_intervals(b'N', N=ord(b'N'))) == [(0, 1)]
assert list(n_intervals(b'n', N=ord(b'N'))) == [(0, 1)]
assert list(n_intervals(b'an', N=ord(b'N'))) == [(1, 2)]
assert list(n_intervals(b'ACGTNNAC', N=ord(b'N'))) == [(4, 6)]
assert list(n_intervals(b'NCGTNNACN', N=ord(b'N'))) == [(0, 1), (4, 6), (8, 9)]
def test_n_intervals():
assert list(n_intervals('')) == []
assert list(n_intervals('N')) == [(0, 1)]
assert list(n_intervals('n')) == [(0, 1)]
assert list(n_intervals('an')) == [(1, 2)]
assert list(n_intervals('ACGTNNAC')) == [(4, 6)]
assert list(n_intervals('NCGTNNACN')) == [(0, 1), (4, 6), (8, 9)]
def test_intervals_complement():
assert list(intervals_complement([], length=10)) == [(0, 10)]
assert list(intervals_complement([(0, 10)], length=10)) == []
assert list(intervals_complement([(0, 2), (4, 6)], length=10)) == [(2, 4), (6,10)]
assert list(intervals_complement([(1, 2), (4, 6)], length=10)) == [(0,1), (2, 4), (6,10)]
assert list(intervals_complement([(0, 1), (3, 10)], length=5)) == [(1, 3)]
assert list(intervals_complement([(2, 10)], length=5)) == [(0, 2)]
assert list(intervals_complement([(0, 10)], length=5)) == []
def test_amino_acid_regex():
for codon1, aa1 in GENETIC_CODE.items():
r = amino_acid_regex(aa1, compile=True)
for codon2, aa2 in GENETIC_CODE.items():
m = r.match(codon2)
assert bool(m) == (aa1 == aa2)
if m:
assert m.group(0) == codon2
def test_nt_to_aa():
assert nt_to_aa('') == ''
assert nt_to_aa('A') == '*'
assert nt_to_aa('AC') == '*'
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