def get_snps(coordinates: List[Tuple[str, int]], genotyper: Genotyper, get_counts=Callable[[str, int], Dict[str, int]]) -> List[SNP]:
result: List[SNP] = []
for chromosome, position in coordinates:
counts = get_counts(chromosome, position)
genotype = genotyper.genotype(counts=counts)
result.append(SNP(chromosome=chromosome, position=position, counts=counts, genotype=genotype))
return result
def setUp(self):
self.snps = [
SNP(chromosome='chr1',
position=1000,
genotype='AA',
counts={
'A': 46,
'C': 1,
'G': 3,
'T': 0
}),
SNP(chromosome='chr2',
position=5000,
genotype='GT',
counts={
'A': 2,
'C': 0,
'G': 18,
'T': 30
})
]
def test_count_unknown_base_raises_exception(self):
snp = SNP(chromosome='chr1', position=1000, genotype='AA', counts={'A': 95, 'C': 1, 'G': 3, 'T': 1})
with self.assertRaises(UnknownBaseError):
snp.count('N')
def test_count(self):
snp = SNP(chromosome='chr19', position=230, genotype='AC', counts={'A': 30, 'C': 22, 'G': 7, 'T': 9})
self.assertEqual(snp.count('A'), 30)
self.assertEqual(snp.count('C'), 22)
self.assertEqual(snp.count('G'), 7)
self.assertEqual(snp.count('T'), 9)
def test_off_genotype_frequency_at_non_genotyped_site_raises_exception(self):
snp = SNP(chromosome='chr1', position=1000, genotype=None, counts={'A': 1, 'C': 2, 'G': 0, 'T': 1})
with self.assertRaises(MissingGenotypeError):
snp.off_genotype_frequency()
def test_off_genotype_frequency_heterozygote_site(self):
snp = SNP(chromosome='chr2', position=5000, genotype='GT', counts={'A': 3, 'C': 2, 'G': 25, 'T': 20})
self.assertEqual(snp.off_genotype_frequency(), 0.1)
def test_off_genotype_frequency_homozygote_site(self):
snp = SNP(chromosome='chr1', position=1000, genotype='AA', counts={'A': 95, 'C': 1, 'G': 3, 'T': 1})
self.assertEqual(snp.off_genotype_frequency(), 0.05)
def test_major_allele_frequency_at_uncovered_position(self):
snp = SNP(chromosome='chr1', position=1000, genotype=None, counts={'A': 0, 'C': 0, 'G': 0, 'T': 0})
self.assertEqual(snp.major_allele_frequency(), 0.0)
def test_is_heterozygote(self):
self.assertFalse(SNP(chromosome='chr1', position=1000, genotype='AA', counts={'A': 95, 'C': 1, 'G': 3, 'T': 1}).is_heterozygote())
self.assertTrue(SNP(chromosome='chr2', position=5000, genotype='GT', counts={'A': 0, 'C': 0, 'G': 35, 'T': 25}).is_heterozygote())
self.assertFalse(SNP(chromosome='chr1', position=1000, genotype=None, counts={'A': 0, 'C': 0, 'G': 0, 'T': 0}).is_heterozygote())
def setUp(self):
self.snp = SNP(chromosome='chr1', position=1000, genotype='AA', counts={'A': 95, 'C': 1, 'G': 3, 'T': 1})
class TestSNP(unittest.TestCase):
def setUp(self):
self.snp = SNP(chromosome='chr1', position=1000, genotype='AA', counts={'A': 95, 'C': 1, 'G': 3, 'T': 1})
def test_create_snp(self):
self.assertEqual(self.snp._chromosome, 'chr1')
self.assertEqual(self.snp._position, 1000)
self.assertEqual(self.snp._genotype, 'AA')
self.assertEqual(self.snp._counts, {'A': 95, 'C': 1, 'G': 3, 'T': 1})
def test_get_genotype(self):
self.assertEqual(self.snp.genotype, 'AA')
def test_get_depth(self):
self.assertEqual(self.snp.depth, 100)
def test_is_homozygote(self):
self.assertTrue(SNP(chromosome='chr1', position=1000, genotype='AA', counts={'A': 95, 'C': 1, 'G': 3, 'T': 1}).is_homozygote())
self.assertFalse(SNP(chromosome='chr2', position=5000, genotype='GT', counts={'A': 0, 'C': 0, 'G': 35, 'T': 25}).is_homozygote())
self.assertFalse(SNP(chromosome='chr1', position=1000, genotype=None, counts={'A': 0, 'C': 0, 'G': 0, 'T': 0}).is_homozygote())
def test_is_heterozygote(self):
self.assertFalse(SNP(chromosome='chr1', position=1000, genotype='AA', counts={'A': 95, 'C': 1, 'G': 3, 'T': 1}).is_heterozygote())
self.assertTrue(SNP(chromosome='chr2', position=5000, genotype='GT', counts={'A': 0, 'C': 0, 'G': 35, 'T': 25}).is_heterozygote())
self.assertFalse(SNP(chromosome='chr1', position=1000, genotype=None, counts={'A': 0, 'C': 0, 'G': 0, 'T': 0}).is_heterozygote())
def test_minor_allele(self):
self.assertEqual(self.snp.minor_allele, 'G')
def test_major_allele(self):
self.assertEqual(self.snp.major_allele, 'A')
def test_minor_allele_frequency(self):
self.assertEqual(self.snp.minor_allele_frequency(), 0.03)
def test_minor_allele_frequency_at_uncovered_position(self):
snp = SNP(chromosome='chr1', position=1000, genotype=None, counts={'A': 0, 'C': 0, 'G': 0, 'T': 0})
self.assertEqual(snp.minor_allele_frequency(), 0.0)
def test_major_allele_frequency(self):
self.assertEqual(self.snp.major_allele_frequency(), 0.95)
def test_major_allele_frequency_at_uncovered_position(self):
snp = SNP(chromosome='chr1', position=1000, genotype=None, counts={'A': 0, 'C': 0, 'G': 0, 'T': 0})
self.assertEqual(snp.major_allele_frequency(), 0.0)
def test_off_genotype_frequency_homozygote_site(self):
snp = SNP(chromosome='chr1', position=1000, genotype='AA', counts={'A': 95, 'C': 1, 'G': 3, 'T': 1})
self.assertEqual(snp.off_genotype_frequency(), 0.05)
def test_off_genotype_frequency_heterozygote_site(self):
snp = SNP(chromosome='chr2', position=5000, genotype='GT', counts={'A': 3, 'C': 2, 'G': 25, 'T': 20})
self.assertEqual(snp.off_genotype_frequency(), 0.1)
def test_off_genotype_frequency_at_non_genotyped_site_raises_exception(self):
snp = SNP(chromosome='chr1', position=1000, genotype=None, counts={'A': 1, 'C': 2, 'G': 0, 'T': 1})
with self.assertRaises(MissingGenotypeError):
snp.off_genotype_frequency()
def test_count(self):
snp = SNP(chromosome='chr19', position=230, genotype='AC', counts={'A': 30, 'C': 22, 'G': 7, 'T': 9})
self.assertEqual(snp.count('A'), 30)
self.assertEqual(snp.count('C'), 22)
self.assertEqual(snp.count('G'), 7)
self.assertEqual(snp.count('T'), 9)
def test_count_unknown_base_raises_exception(self):
snp = SNP(chromosome='chr1', position=1000, genotype='AA', counts={'A': 95, 'C': 1, 'G': 3, 'T': 1})
with self.assertRaises(UnknownBaseError):
snp.count('N')
def test_snp_string_representation(self):
self.assertEqual(self.snp.__str__(), 'chr1:1000')