def test_spectrum_alleles_count():
with Capturing() as out:
calc.main(["calc", "spectrum", "test_data/test.vcf.gz"])
assert round(float(out[-2].split("\t")[1]), 5) == 0.03571
def test_sample_hom_gt():
with Capturing() as out:
calc.main(["calc", "sample_hom_gt", "test_data/test.vcf.gz"])
assert out[0] == 'sample\tfreq_of_gt\tn_gt_at_freq'
assert out[10] == 'AB1\t10\t8'
def test_spectrum_genotypes_count():
with Capturing() as out:
calc.main(["calc", "genotypes", "test_data/test.vcf.gz"])
assert out[0] == 'n\tref\thet\talt\tmis'
assert out[-1] == '1\t0\t0\t12\t2'
def test_spectrum_genotypes_frequency():
with Capturing() as out:
calc.main(["calc", "genotypes", "test_data/test.vcf.gz"])
assert out[-1] == '1\t0\t0\t12\t2'
def test_sample_hom_gt():
with Capturing() as out:
calc.main(["calc", "sample_hom_gt", "test_data/test.vcf.gz"])
assert out[0] == 'sample\tfreq_of_gt\tn_gt_at_freq'
assert out[10] == 'QG536\t10\t11'
def test_spectrum_alleles_count():
with Capturing() as out:
calc.main(["calc", "spectrum", "test_data/test.vcf.gz"])
assert out[-2] == '23\t0.0357142857143'
def test_spectrum_genotypes_frequency():
with Capturing() as out:
calc.main(["calc", "genotypes", "test_data/test.vcf.gz"])
assert out[-1] == '1\t9\t2\t1\t2'
def test_spectrum_genotypes_count():
with Capturing() as out:
calc.main(["calc", "genotypes", "test_data/test.vcf.gz"])
assert out[0] == 'n\tref\thet\talt\tmis'
assert out[-1] == '1\t9\t2\t1\t2'
def test_spectrum_alleles_count():
with Capturing() as out:
calc.main(["calc", "spectrum", "data/test.vcf.gz"])
assert out[-2] == '23\t0.0357142857143'