def test_merge_simple_var(self):
vars1 = MockList([{'chrom': '1', 'pos': 1, 'ref': b'A', 'alt': [b'T'],
'gts': numpy.array([[0, 0], [1, 1]]), 'qual': 34}])
vars2 = MockList([{'chrom': '1', 'pos': 1, 'ref': b'A', 'alt': [b'T'],
'gts': numpy.array([[0, 0], [1, 1]]), 'qual': 35}])
vars1.samples = ['a', 'b']
vars2.samples = ['c', 'd']
merger = MockMerger(gt_shape=(4, 2))
variation = VarMerger._merge_vars(merger, vars1[0], vars2[0])
exp = {'gts': [[0, 0], [1, 1], [0, 0], [1, 1]], 'pos': 1,
'ref': b'A', 'chrom': '1', 'alt': [b'T'], 'qual': 34}
self.var_is_equal(exp, variation)
vars1 = MockList([{'chrom': '1', 'pos': 1, 'ref': b'A', 'alt': [b'T'],
'gts': numpy.array([[0, 0], [1, 1]]), 'qual': 21}])
vars2 = MockList([{'chrom': '1', 'pos': 2, 'ref': b'A', 'alt': [b'T'],
'gts': numpy.array([[0, 0], [1, 1]]), 'qual': 21}])
vars1.samples = ['a', 'b']
vars2.samples = ['c', 'd']
variation = VarMerger._merge_vars(merger, vars1[0], None)
exp = {'gts': [[0, 0], [1, 1], [-1, -1], [-1, -1]], 'pos': 1,
'ref': b'A', 'chrom': '1', 'alt': [b'T'], 'qual': 21}
self.var_is_equal(exp, variation)
variation = VarMerger._merge_vars(merger, None, vars2[0])
exp = {'gts': [[-1, -1], [-1, -1], [0, 0], [1, 1]], 'pos': 2,
'ref': b'A', 'chrom': '1', 'alt': [b'T'], 'qual': 21}
self.var_is_equal(exp, variation)
def test_merge_simple_var(self):
vars1 = MockList([{'chrom': '1', 'pos': 1, 'ref': b'A', 'alt': [b'T'],
'gts': numpy.array([[0, 0], [1, 1]]), 'qual': 34}])
vars2 = MockList([{'chrom': '1', 'pos': 1, 'ref': b'A', 'alt': [b'T'],
'gts': numpy.array([[0, 0], [1, 1]]), 'qual': 35}])
vars1.samples = ['a', 'b']
vars2.samples = ['c', 'd']
merger = MockMerger(gt_shape=(4, 2))
variation = VarMerger._merge_vars(merger, vars1[0], vars2[0])
exp = {'gts': [[0, 0], [1, 1], [0, 0], [1, 1]], 'pos': 1,
'ref': b'A', 'chrom': '1', 'alt': [b'T'], 'qual': 34}
self.var_is_equal(exp, variation)
vars1 = MockList([{'chrom': '1', 'pos': 1, 'ref': b'A', 'alt': [b'T'],
'gts': numpy.array([[0, 0], [1, 1]]), 'qual': 21}])
vars2 = MockList([{'chrom': '1', 'pos': 2, 'ref': b'A', 'alt': [b'T'],
'gts': numpy.array([[0, 0], [1, 1]]), 'qual': 21}])
vars1.samples = ['a', 'b']
vars2.samples = ['c', 'd']
variation = VarMerger._merge_vars(merger, vars1[0], None)
exp = {'gts': [[0, 0], [1, 1], [-1, -1], [-1, -1]], 'pos': 1,
'ref': b'A', 'chrom': '1', 'alt': [b'T'], 'qual': 21}
self.var_is_equal(exp, variation)
variation = VarMerger._merge_vars(merger, None, vars2[0])
exp = {'gts': [[-1, -1], [-1, -1], [0, 0], [1, 1]], 'pos': 2,
'ref': b'A', 'chrom': '1', 'alt': [b'T'], 'qual': 21}
self.var_is_equal(exp, variation)
def test_merge_complex_var(self):
# Deletion
vars1 = MockList([{'chrom': '1', 'pos': 1, 'ref': b'C',
'alt': [b'CAAG', b'CAAA'],
'gts': numpy.array([[0, 0], [1, 1]]),
'qual': 21}])
vars2 = MockList([{'chrom': '1', 'pos': 1, 'ref': b'C', 'alt': [b'A'],
'gts': numpy.array([[0, 0], [1, 1]]),
'qual': None}])
vars1.samples = ['a', 'b']
vars2.samples = ['c', 'd']
merger = MockMerger(gt_shape=(4, 2))
variation = VarMerger._merge_vars(merger, vars1[0], vars2[0])
exp = {'gts': [[0, 0], [1, 1], [0, 0], [3, 3]], 'pos': 1,
'ref': b'C', 'chrom': '1', 'alt': [b'CAAG', b'CAAA', b'A'],
'qual': None}
self.var_is_equal(exp, variation)
vars1 = MockList([{'chrom': '1', 'pos': 1, 'ref': b'ATT',
'alt': [b'T'], 'gts': numpy.array([[0, 0], [1, 1]]),
'qual': 21}])
vars2 = MockList([{'chrom': '1', 'pos': 2, 'ref': b'T', 'alt': [b'A'],
'gts': numpy.array([[0, 0], [1, 1]]),
'qual': None}])
vars1.samples = ['a', 'b']
vars2.samples = ['c', 'd']
merger = MockMerger(gt_shape=(4, 2))
variation = VarMerger._merge_vars(merger, vars1[0], vars2[0])
exp = {'gts': [[0, 0], [1, 1], [0, 0], [2, 2]], 'pos': 1,
'ref': b'ATT', 'chrom': '1', 'alt': [b'T', b'AAT'],
'qual': None}
self.var_is_equal(exp, variation)
vars1 = MockList([{'chrom': '1', 'pos': 1, 'ref': b'C',
'alt': [b'CGGT'],
'gts': numpy.array([[0, 0], [1, 1]]),
'qual': 21}])
vars2 = MockList([{'chrom': '1', 'pos': 2, 'ref': b'C',
'alt': [b'T'],
'gts': numpy.array([[0, 0], [1, 1]]),
'qual': None}])
vars1.samples = ['a', 'b']
vars2.samples = ['c', 'd']
merger = MockMerger(gt_shape=(4, 2))
try:
variation = merger._merge_vars(vars1[0], vars2[0])
self.fail('MalformedVariationError expected')
except MalformedVariationError:
pass
def test_merge_complex_var(self):
# Deletion
vars1 = MockList([{'chrom': '1', 'pos': 1, 'ref': b'C',
'alt': [b'CAAG', b'CAAA'],
'gts': numpy.array([[0, 0], [1, 1]]),
'qual': 21}])
vars2 = MockList([{'chrom': '1', 'pos': 1, 'ref': b'C', 'alt': [b'A'],
'gts': numpy.array([[0, 0], [1, 1]]),
'qual': None}])
vars1.samples = ['a', 'b']
vars2.samples = ['c', 'd']
merger = MockMerger(gt_shape=(4, 2))
variation = VarMerger._merge_vars(merger, vars1[0], vars2[0])
exp = {'gts': [[0, 0], [1, 1], [0, 0], [3, 3]], 'pos': 1,
'ref': b'C', 'chrom': '1', 'alt': [b'CAAG', b'CAAA', b'A'],
'qual': None}
self.var_is_equal(exp, variation)
vars1 = MockList([{'chrom': '1', 'pos': 1, 'ref': b'ATT',
'alt': [b'T'], 'gts': numpy.array([[0, 0], [1, 1]]),
'qual': 21}])
vars2 = MockList([{'chrom': '1', 'pos': 2, 'ref': b'T', 'alt': [b'A'],
'gts': numpy.array([[0, 0], [1, 1]]),
'qual': None}])
vars1.samples = ['a', 'b']
vars2.samples = ['c', 'd']
merger = MockMerger(gt_shape=(4, 2))
variation = VarMerger._merge_vars(merger, vars1[0], vars2[0])
exp = {'gts': [[0, 0], [1, 1], [0, 0], [2, 2]], 'pos': 1,
'ref': b'ATT', 'chrom': '1', 'alt': [b'T', b'AAT'],
'qual': None}
self.var_is_equal(exp, variation)
vars1 = MockList([{'chrom': '1', 'pos': 1, 'ref': b'C',
'alt': [b'CGGT'],
'gts': numpy.array([[0, 0], [1, 1]]),
'qual': 21}])
vars2 = MockList([{'chrom': '1', 'pos': 2, 'ref': b'C',
'alt': [b'T'],
'gts': numpy.array([[0, 0], [1, 1]]),
'qual': None}])
vars1.samples = ['a', 'b']
vars2.samples = ['c', 'd']
merger = MockMerger(gt_shape=(4, 2))
try:
variation = merger._merge_vars(vars1[0], vars2[0])
self.fail('MalformedVariationError expected')
except MalformedVariationError:
pass
def test_merge_with_depth(self):
vars1 = MockList([{'chrom': '1', 'pos': 1, 'ref': b'A', 'alt': [b'T'],
'gts': numpy.array([[0, 0], [1, 1]]),
'dp': numpy.array([1, 1])}])
vars2 = MockList([{'chrom': '1', 'pos': 1, 'ref': b'A', 'alt': [b'T'],
'gts': numpy.array([[0, 0], [1, 1]]),
'dp': numpy.array([20, 20])}])
vars1.samples = ['a', 'b']
vars2.samples = ['c', 'd']
merger = MockMerger(gt_shape=(4, 2))
variation = VarMerger._merge_vars(merger, vars1[0], vars2[0])
exp = {'gts': [[0, 0], [1, 1], [0, 0], [1, 1]], 'pos': 1,
'ref': b'A', 'chrom': '1', 'alt': [b'T'], 'dp': [1, 1, 20, 20]}
self.var_is_equal(exp, variation)
# merge the same var with depth
h5_1 = VariationsH5(join(TEST_DATA_DIR, 'format_def.h5'), "r")
h5_2 = VariationsH5(join(TEST_DATA_DIR, 'format_def.h5'), "r")
merger = VarMerger(h5_1, h5_2, max_field_lens={'alt': 3},
ignore_complex_overlaps=True,
check_ref_matches=False, ignore_non_matching=True)
new_vars = VariationsArrays(ignore_overflows=True,
ignore_undefined_fields=True)
first_snv_merged_depth = numpy.array([1, 8, 5, 1, 8, 5],
dtype=numpy.int16)
depth = list(merger.variations)[0][8][1]
assert depth[0] == b'DP'
assert numpy.all(depth[1] == first_snv_merged_depth)
new_vars.put_vars(merger)
assert '/calls/DP' in new_vars.keys()
assert numpy.all(new_vars['/calls/DP'][0] == first_snv_merged_depth)
def test_merge_with_depth(self):
vars1 = MockList([{'chrom': '1', 'pos': 1, 'ref': b'A', 'alt': [b'T'],
'gts': numpy.array([[0, 0], [1, 1]]),
'dp': numpy.array([1, 1])}])
vars2 = MockList([{'chrom': '1', 'pos': 1, 'ref': b'A', 'alt': [b'T'],
'gts': numpy.array([[0, 0], [1, 1]]),
'dp': numpy.array([20, 20])}])
vars1.samples = ['a', 'b']
vars2.samples = ['c', 'd']
merger = MockMerger(gt_shape=(4, 2))
variation = VarMerger._merge_vars(merger, vars1[0], vars2[0])
exp = {'gts': [[0, 0], [1, 1], [0, 0], [1, 1]], 'pos': 1,
'ref': b'A', 'chrom': '1', 'alt': [b'T']}
self.var_is_equal(exp, variation)