def test_call_filtered_set(self):
site_filters = generate_filter(SOME_CHROMOSOMES_FILTERS)
under_test = FilteringVectorGenotypeCallset(site_filters=site_filters,
callset=self.callset)
actual = under_test.gt(CHROMOSOME_1)
self.assertTrue((allel.GenotypeVector([[1, 1]]) == actual).all())
actual = under_test.gt(CHROMOSOME_2)
self.assertTrue((allel.GenotypeVector([[0, 0], [2,
0]]) == actual).all())
def test_call_set(self):
zarr_group = generate_gt_data(SAMPLE_A, SOME_CHROMOSOMES_GT)
under_test = VectorGenotypeCallset(sample=SAMPLE_A, callset=zarr_group)
actual = under_test.gt(CHROMOSOME_1)
self.assertTrue(
(allel.GenotypeVector(CHROMOSOME_1_GT) == actual).all())
actual = under_test.gt(CHROMOSOME_2)
self.assertTrue(
(allel.GenotypeVector(CHROMOSOME_2_GT) == actual).all())
def test_compute_hom_alt_mismatch(self, value):
control, test, expected = value
lgt = allel.GenotypeVector([control])
rgt = allel.GenotypeVector([test])
actual = compute_hom_alt_mismatch(control=lgt,
test=rgt,
recorder=self.recorder)
self.assertEqual(expected, actual)
self.assertCountEqual(
self.recorder.record.call_args_list,
[call(HOMOZIGOUS_ALTERNATE_CATEGORY, MISMATCH_CATEGORY, expected)])
def readData(dir):
fs=os.listdir(dir)
for f in fs:
bf=tbf.copy_template(outdir+f+".bloom")
try:
input=''.join([dir, f])
callset=allel.read_vcf(input, fields=['variants/CHROM','variants/POS', 'calldata/GT'], types={'calldata/GT':'i2'},
fills={'calldata/GT':2})
chrom=callset['variants/CHROM']
pos=callset['variants/POS']
gt=allel.GenotypeArray(callset['calldata/GT'])
for i in range(len(chrom)):
position='|'.join([chrom[i], str(pos[i])])
gv=allel.GenotypeVector(gt[i])
key1=0
key2=0
if gv[0][0] ==0|gv[0][0] ==1|gv[0][0] ==2 :
key1=gv[0][0]
print("key1:"+str(key1))
if gv[0][1] ==0|gv[0][1] ==1|gv[0][1] ==2:
key2=gv[0][1]
sum=key1|key2
key='|'.join([position, str(sum)])
bf.add(key)
except Exception as err:
print(f)
print(err)
bf.close()
def setUp(self) -> None:
self.callset = MagicMock()
self.callset.gt.side_effect = lambda chromosome: allel.GenotypeVector(
SOME_CHROMOSOMES_GT[chromosome])
def gt(self, chromosome: str) -> allel.GenotypeVector:
gt = self.callset[GT_PATH_FORMAT.format(sample=self.sample,
chromosome=chromosome)]
return allel.GenotypeVector(gt[:, ONLY_ONE_SAMPLE_IN_VECTOR_GT_ZARR])