def test_create_hdf5_with_chunks(self):
hdf5 = VariationsH5(join(TEST_DATA_DIR, '1000snps.hdf5'), mode='r')
out_fhand = NamedTemporaryFile(suffix='.hdf5')
out_fpath = out_fhand.name
out_fhand.close()
hdf5_2 = VariationsH5(out_fpath, 'w')
try:
hdf5_2.put_chunks(hdf5.iterate_chunks())
assert sorted(hdf5_2['calls'].keys()) == ['DP', 'GQ', 'GT', 'HQ']
assert numpy.all(hdf5['/calls/GT'][:] == hdf5_2['/calls/GT'][:])
finally:
os.remove(out_fpath)
hdf5 = VariationsH5(join(TEST_DATA_DIR, '1000snps.hdf5'), mode='r')
out_fhand = NamedTemporaryFile(suffix='.hdf5')
out_fpath = out_fhand.name
out_fhand.close()
hdf5_2 = VariationsH5(out_fpath, 'w')
try:
hdf5_2.put_chunks(hdf5.iterate_chunks(kept_fields=['/calls/GT']))
assert list(hdf5_2['calls'].keys()) == ['GT']
assert numpy.all(hdf5['/calls/GT'][:] == hdf5_2['/calls/GT'][:])
finally:
os.remove(out_fpath)
hdf5 = VariationsH5(join(TEST_DATA_DIR, 'ril.hdf5'), mode='r')
hdf5_2 = VariationsArrays()
hdf5_2.put_chunks(hdf5.iterate_chunks(random_sample_rate=0.2))
_, prob = ttest_ind(hdf5['/variations/pos'][:],
hdf5_2['/variations/pos'][:])
assert prob > 0.05
assert hdf5_2.num_variations / hdf5.num_variations - 0.2 < 0.1
chrom = hdf5_2['/variations/chrom'][0]
pos = hdf5_2['/variations/pos'][0]
index = PosIndex(hdf5)
idx = index.index_pos(chrom, pos)
old_snp = hdf5['/calls/GT'][idx]
new_snp = hdf5_2['/calls/GT'][0]
assert numpy.all(old_snp == new_snp)
# putting empty chunks
hdf5_2.put_chunks(None)
hdf5_2.put_chunks([])
chunk = hdf5.get_chunk(slice(1000, None))
hdf5_2.put_chunks([chunk])
old_snp = hdf5['/calls/DP'][idx]
new_snp = hdf5_2['/calls/DP'][0]
assert numpy.all(old_snp == new_snp)
hdf5 = VariationsH5(join(TEST_DATA_DIR, '1000snps.hdf5'), mode='r')
hdf5_2 = VariationsArrays()
hdf5_2.put_chunks(hdf5.iterate_chunks(random_sample_rate=0))
assert hdf5_2.num_variations == 0
hdf5 = VariationsH5(join(TEST_DATA_DIR, 'ril.hdf5'), mode='r')
hdf5_3 = VariationsArrays()
hdf5_3.put_chunks(hdf5.iterate_chunks(random_sample_rate=0.01))
def test_create_hdf5_with_chunks(self):
hdf5 = VariationsH5(join(TEST_DATA_DIR, '1000snps.hdf5'), mode='r')
out_fhand = NamedTemporaryFile(suffix='.hdf5')
out_fpath = out_fhand.name
out_fhand.close()
hdf5_2 = VariationsH5(out_fpath, 'w')
try:
hdf5_2.put_chunks(hdf5.iterate_chunks())
assert sorted(hdf5_2['calls'].keys()) == ['DP', 'GQ', 'GT', 'HQ']
assert numpy.all(hdf5['/calls/GT'][:] == hdf5_2['/calls/GT'][:])
finally:
os.remove(out_fpath)
hdf5 = VariationsH5(join(TEST_DATA_DIR, '1000snps.hdf5'), mode='r')
out_fhand = NamedTemporaryFile(suffix='.hdf5')
out_fpath = out_fhand.name
out_fhand.close()
hdf5_2 = VariationsH5(out_fpath, 'w')
try:
hdf5_2.put_chunks(hdf5.iterate_chunks(kept_fields=['/calls/GT']))
assert list(hdf5_2['calls'].keys()) == ['GT']
assert numpy.all(hdf5['/calls/GT'][:] == hdf5_2['/calls/GT'][:])
finally:
os.remove(out_fpath)
hdf5 = VariationsH5(join(TEST_DATA_DIR, 'ril.hdf5'), mode='r')
hdf5_2 = VariationsArrays()
hdf5_2.put_chunks(hdf5.iterate_chunks(random_sample_rate=0.2))
_, prob = scipy.stats.ttest_ind(hdf5['/variations/pos'][:],
hdf5_2['/variations/pos'][:])
assert prob > 0.05
assert hdf5_2.num_variations / hdf5.num_variations - 0.2 < 0.1
chrom = hdf5_2['/variations/chrom'][0]
pos = hdf5_2['/variations/pos'][0]
index = PosIndex(hdf5)
idx = index.index_pos(chrom, pos)
old_snp = hdf5['/calls/GT'][idx]
new_snp = hdf5_2['/calls/GT'][0]
assert numpy.all(old_snp == new_snp)
# putting empty chunks
hdf5_2.put_chunks(None)
hdf5_2.put_chunks([])
chunk = hdf5.get_chunk(slice(1000, None))
hdf5_2.put_chunks([chunk])
old_snp = hdf5['/calls/DP'][idx]
new_snp = hdf5_2['/calls/DP'][0]
assert numpy.all(old_snp == new_snp)
hdf5 = VariationsH5(join(TEST_DATA_DIR, '1000snps.hdf5'), mode='r')
hdf5_2 = VariationsArrays()
hdf5_2.put_chunks(hdf5.iterate_chunks(random_sample_rate=0))
assert hdf5_2.num_variations == 0
hdf5 = VariationsH5(join(TEST_DATA_DIR, 'ril.hdf5'), mode='r')
hdf5_3 = VariationsArrays()
hdf5_3.put_chunks(hdf5.iterate_chunks(random_sample_rate=0.01))
def test_index(self):
snps = VariationsArrays()
chroms = [1, 1, 1, 2, 2, 2, 3, 3, 3, 4, 4, 4]
pos = [1, 2, 3, 1, 2, 3, 1, 2, 3, 2, 4, 6]
snps[CHROM_FIELD] = numpy.array(chroms)
snps[POS_FIELD] = numpy.array(pos)
index = PosIndex(snps)
assert index.index_pos(1, 1) == 0
assert index.index_pos(2, 1) == 3
assert index.index_pos(3, 1) == 6
assert index.index_pos(4, 1) == 9
assert index.index_pos(4, 2) == 9
assert index.index_pos(4, 3) == 10
assert index.index_pos(4, 4) == 10
assert index.get_chrom_range_index(1) == (0, 2)
assert index.get_chrom_range_pos(1) == (1, 3)
assert index.covered_length == 10
def test_index(self):
snps = VariationsArrays()
chroms = [1, 1, 1, 2, 2, 2, 3, 3, 3, 4, 4, 4]
pos = [1, 2, 3, 1, 2, 3, 1, 2, 3, 2, 4, 6]
snps['/variations/chrom'] = numpy.array(chroms)
snps['/variations/pos'] = numpy.array(pos)
index = PosIndex(snps)
assert index.index_pos(1, 1) == 0
assert index.index_pos(2, 1) == 3
assert index.index_pos(3, 1) == 6
assert index.index_pos(4, 1) == 9
assert index.index_pos(4, 2) == 9
assert index.index_pos(4, 3) == 10
assert index.index_pos(4, 4) == 10
assert index.get_chrom_range_index(1) == (0, 2)
assert index.get_chrom_range_pos(1) == (1, 3)
assert index.covered_length == 10
def pos_index(self):
if self._index is None:
self._index = PosIndex(self)
return self._index
