def test_invalid_access():
ga = create_genomic_array({'chr10': 300},
stranded=False,
typecode='int8',
storage='ndarray')
with pytest.raises(Exception):
# access only via genomic interval
ga[1]
with pytest.raises(Exception):
# access only via genomic interval and condition
ga[1] = 1
ga = create_genomic_array({'chr10': 300},
stranded=False,
typecode='int8',
storage='sparse')
with pytest.raises(Exception):
# access only via genomic interval
ga[1]
with pytest.raises(Exception):
# access only via genomic interval and condition
ga[1] = 1
def test_bwga_instance_unstranded_taged(tmpdir):
os.environ['JANGGU_OUTPUT'] = tmpdir.strpath
iv = GenomicInterval('chr10', 100, 120, '.')
ga = create_genomic_array({'chr10': 300},
stranded=False,
typecode='int8',
storage='ndarray',
datatags='test_bwga_instance_unstranded')
with pytest.raises(Exception):
# access only via genomic interval
ga[1]
with pytest.raises(Exception):
# access only via genomic interval and condition
ga[1] = 1
np.testing.assert_equal(ga[iv].shape, (20, 1, 1))
np.testing.assert_equal(ga[iv], np.zeros((20, 1, 1)))
ga[iv, 0] = np.ones((20, 1))
np.testing.assert_equal(ga[iv], np.ones((20, 1, 1)))
np.testing.assert_equal(ga[iv].sum(), 20)
iv = GenomicInterval('chr10', 0, 300, '.')
np.testing.assert_equal(ga[iv].sum(), 20)
def test_tmp_normalization(tmpdir):
os.environ['JANGGU_OUTPUT'] = tmpdir.strpath
def loading(garray):
garray[GenomicInterval('chr1', 0, 150),
0] = np.repeat(10, 150).reshape(-1, 1)
garray[GenomicInterval('chr2', 0, 300),
0] = np.repeat(1, 300).reshape(-1, 1)
return garray
for store in ['ndarray', 'hdf5']:
ga = create_genomic_array({
'chr1': 150,
'chr2': 300
},
stranded=False,
typecode='float32',
storage=store,
cache=True,
resolution=50,
loader=loading,
collapser='sum',
normalizer=get_normalizer('tpm'))
np.testing.assert_allclose(
ga[GenomicInterval('chr1', 100, 101)],
np.asarray([[[10 * 1000 / 50 * 1e6 / (720.)]]]))
np.testing.assert_allclose(
ga[GenomicInterval('chr2', 100, 101)],
np.asarray([[[1 * 1000 / 50 * 1e6 / (720.)]]]))
def test_resolution_negative():
with pytest.raises(Exception):
ga = create_genomic_array({'chr10': 300},
stranded=True,
typecode='int8',
storage='ndarray',
cache=False,
resolution=-1)
def test_hdf5_no_cache():
with pytest.raises(Exception):
# cache must be True
ga = create_genomic_array({'chr10': 300},
stranded=True,
typecode='int8',
storage='hdf5',
cache=False)
def test_invalid_storage():
with pytest.raises(Exception):
ga = create_genomic_array(GenomicIndexer.create_from_genomesize(
{'chr10': 300}),
stranded=True,
typecode='int8',
storage='storgae',
resolution=1,
cache=False)
def test_hdf5_no_cache():
with pytest.raises(Exception):
# cache must be True
ga = create_genomic_array(GenomicIndexer.create_from_genomesize(
{'chr10': 300}),
stranded=True,
typecode='int8',
storage='hdf5',
cache=None)
def test_bwga_instance_unstranded(tmpdir):
iv = GenomicInterval('chr10', 100, 120, '.')
ga = create_genomic_array({'chr10': 300},
stranded=False,
typecode='int8',
storage='ndarray',
cache=False)
np.testing.assert_equal(ga[iv].shape, (20, 1, 1))
np.testing.assert_equal(ga[iv], np.zeros((20, 1, 1)))
ga[iv, 0] = 1
np.testing.assert_equal(ga[iv], np.ones((20, 1, 1)))
np.testing.assert_equal(ga[iv].sum(), 20)
iv = GenomicInterval('chr10', 0, 300, '.')
np.testing.assert_equal(ga[iv].sum(), 20)
def test_bwga_instance_stranded(tmpdir):
os.environ['JANGGU_OUTPUT'] = tmpdir.strpath
iv = GenomicInterval('chr10', 100, 120, '+')
ga = create_genomic_array({'chr10': 300},
stranded=True,
typecode='int8',
storage='ndarray')
np.testing.assert_equal(ga[iv].shape, (20, 2, 1))
np.testing.assert_equal(ga[iv], np.zeros((20, 2, 1)))
ga[iv, 0] = 1
x = np.zeros((20, 2, 1))
x[:, :1, :] = np.ones((20, 1, 1))
np.testing.assert_equal(ga[iv], x)
np.testing.assert_equal(ga[iv].sum(), 20)
iv = GenomicInterval('chr10', 0, 300)
np.testing.assert_equal(ga[iv].sum(), 20)
def test_bwga_instance_stranded_notcached(tmpdir):
iv = GenomicInterval('chr10', 100, 120, '+')
ga = create_genomic_array({'chr10': 300},
stranded=True,
typecode='int8',
storage='ndarray',
cache=False)
np.testing.assert_equal(ga[iv].shape, (20, 2, 1))
np.testing.assert_equal(ga[iv], np.zeros((20, 2, 1)))
x = np.zeros((20, 2, 1))
x[:, :1, :] = 1
ga[iv, 0] = x[:, :, 0]
np.testing.assert_equal(ga[iv], x)
np.testing.assert_equal(ga[iv].sum(), 20)
iv = GenomicInterval('chr10', 0, 300)
np.testing.assert_equal(ga[iv].sum(), 20)
def test_perctrim(tmpdir):
os.environ['JANGGU_OUTPUT'] = tmpdir.strpath
def loading(garray):
garray[Interval('chr1', 0, 150),
0] = np.random.normal(loc=10, size=150).reshape(-1, 1)
garray[Interval('chr2', 0, 300),
0] = np.random.normal(loc=100, size=300).reshape(-1, 1)
return garray
for store in ['ndarray', 'hdf5']:
ga = create_genomic_array(GenomicIndexer.create_from_genomesize({
'chr1':
150,
'chr2':
300
}),
stranded=False,
typecode='float32',
storage=store,
cache="cache_file",
loader=loading,
normalizer=['binsizenorm', 'perctrim'])
def test_logzscore_normalization(tmpdir):
os.environ['JANGGU_OUTPUT'] = tmpdir.strpath
def loading(garray):
garray[GenomicInterval('chr1', 0, 150),
0] = np.repeat(10, 150).reshape(-1, 1)
garray[GenomicInterval('chr2', 0, 300),
0] = np.repeat(100, 300).reshape(-1, 1)
return garray
for store in ['ndarray', 'hdf5']:
ga = create_genomic_array({
'chr1': 150,
'chr2': 300
},
stranded=False,
typecode='float32',
storage=store,
cache=True,
loader=loading,
normalizer=get_normalizer('zscorelog'))
np.testing.assert_allclose(ga.weighted_mean(),
np.asarray([0.0]),
rtol=1e-5,
atol=1e-5)
np.testing.assert_allclose(ga.weighted_sd(),
np.asarray([1.]),
rtol=1e-5,
atol=1e-5)
np.testing.assert_allclose(ga[GenomicInterval('chr1', 100, 101)],
np.asarray([[[-1.412641340027806]]]),
rtol=1e-5,
atol=1e-5)
np.testing.assert_allclose(ga[GenomicInterval('chr2', 100, 101)],
np.asarray([[[0.706320670013903]]]),
rtol=1e-5,
atol=1e-5)
def test_check_resolution_collapse_compatibility():
def loading(garray):
garray[GenomicInterval('chr1:0-150', 0, 150),
0] = np.repeat(10, 150).reshape(-1, 1)
garray[GenomicInterval('chr2:0-300', 0, 300),
0] = np.repeat(1, 300).reshape(-1, 1)
return garray
with pytest.raises(Exception):
# Error because resolution=50 but no collapser defined
ga = create_genomic_array({
'chr1': 150,
'chr2': 300
},
stranded=False,
typecode='float32',
storage="ndarray",
cache=False,
resolution=50,
loader=loading,
collapser=None,
normalizer=get_normalizer('tpm'))
with pytest.raises(Exception):
# Error because resolution=50 but no collapser defined
ga = create_genomic_array({
'chr1': 150,
'chr2': 300
},
stranded=False,
typecode='float32',
storage="ndarray",
cache=False,
resolution=None,
loader=loading,
collapser=None,
normalizer=get_normalizer('tpm'))
ga = create_genomic_array({
'chr1:0-150': 150,
'chr2:0-300': 300
},
stranded=False,
typecode='float32',
storage="ndarray",
cache=False,
resolution=1,
loader=loading)
ga = create_genomic_array({
'chr1:0-150': 150,
'chr2:0-300': 300
},
stranded=False,
typecode='float32',
storage="ndarray",
cache=False,
resolution=None,
loader=loading,
collapser='sum')
ga = create_genomic_array({
'chr1:0-150': 150,
'chr2:0-300': 300
},
stranded=False,
typecode='float32',
storage="ndarray",
cache=False,
resolution=None,
loader=loading,
collapser='sum',
normalizer=get_normalizer('tpm'))
def test_check_resolution_collapse_compatibility(tmpdir):
os.environ['JANGGU_OUTPUT'] = tmpdir.strpath
def loading(garray):
garray[Interval('chr1', 0, 150), 0] = np.repeat(10, 150).reshape(-1, 1)
garray[Interval('chr2', 0, 300), 0] = np.repeat(1, 300).reshape(-1, 1)
return garray
with pytest.raises(Exception):
# Error because resolution=50 but no collapser defined
ga = create_genomic_array(GenomicIndexer.create_from_genomesize({
'chr1':
150,
'chr2':
300
}),
stranded=False,
typecode='float32',
storage="ndarray",
cache=None,
resolution=50,
loader=loading,
collapser=None,
normalizer=['tpm'])
with pytest.raises(Exception):
# Error because resolution=None but no collapser defined
ga = create_genomic_array(GenomicIndexer.create_from_genomesize({
'chr1':
150,
'chr2':
300
}),
stranded=False,
typecode='float32',
storage="ndarray",
cache=None,
resolution=None,
loader=loading,
collapser=None,
normalizer=['tpm'])
ga = create_genomic_array(GenomicIndexer.create_from_file(
[
Interval('chr1', 0, 150),
Interval('chr2', 0, 150),
Interval('chr2', 150, 300)
],
binsize=150,
stepsize=None,
),
stranded=False,
typecode='float32',
storage="ndarray",
cache=None,
resolution=1,
loader=loading)
ga = create_genomic_array(GenomicIndexer.create_from_file(
[Interval('chr1', 0, 150),
Interval('chr2', 0, 300)],
binsize=None,
stepsize=None,
collapse=True),
stranded=False,
typecode='float32',
storage="ndarray",
cache='test',
resolution=None,
loader=loading,
store_whole_genome=None,
collapser='sum')
ga = create_genomic_array(GenomicIndexer.create_from_file(
[Interval('chr1', 0, 150),
Interval('chr2', 0, 300)],
binsize=None,
stepsize=None,
collapse=True),
stranded=False,
typecode='float32',
storage="ndarray",
cache=None,
resolution=None,
loader=loading,
collapser='sum',
normalizer=['tpm'])
def test_logzscore_normalization(tmpdir):
os.environ['JANGGU_OUTPUT'] = tmpdir.strpath
def loading(garray):
garray[Interval('chr1', 0, 150), 0] = np.repeat(10, 150).reshape(-1, 1)
garray[Interval('chr2', 0, 300), 0] = np.repeat(100,
300).reshape(-1, 1)
return garray
from janggu.data.genomicarray import LogTransform, ZScore
ga = create_genomic_array(GenomicIndexer.create_from_genomesize({
'chr1': 150,
'chr2': 300
}),
stranded=False,
typecode='float32',
storage='ndarray',
cache=None,
loader=loading)
ga = create_genomic_array(GenomicIndexer.create_from_genomesize({
'chr1': 150,
'chr2': 300
}),
stranded=False,
typecode='float32',
storage='ndarray',
cache=None,
loader=loading,
normalizer=[LogTransform()])
ga = create_genomic_array(GenomicIndexer.create_from_genomesize({
'chr1': 150,
'chr2': 300
}),
stranded=False,
typecode='float32',
storage='ndarray',
cache=None,
loader=loading,
normalizer=[ZScore()])
ga = create_genomic_array(GenomicIndexer.create_from_genomesize({
'chr1': 150,
'chr2': 300
}),
stranded=False,
typecode='float32',
storage='ndarray',
cache=None,
loader=loading,
normalizer=[LogTransform(),
ZScore()])
ga = create_genomic_array(GenomicIndexer.create_from_genomesize({
'chr1': 150,
'chr2': 300
}),
stranded=False,
typecode='float32',
storage='ndarray',
cache=None,
loader=loading,
normalizer=['zscorelog'])
for store in ['ndarray', 'hdf5']:
ga = create_genomic_array(GenomicIndexer.create_from_genomesize({
'chr1':
150,
'chr2':
300
}),
stranded=False,
typecode='float32',
storage=store,
cache="cache_file",
loader=loading,
normalizer=['zscorelog'])
np.testing.assert_allclose(ga.weighted_mean(),
np.asarray([0.0]),
rtol=1e-5,
atol=1e-5)
np.testing.assert_allclose(ga.weighted_sd(),
np.asarray([1.]),
rtol=1e-5,
atol=1e-5)
np.testing.assert_allclose(ga[Interval('chr1', 100, 101)],
np.asarray([[[-1.412641340027806]]]),
rtol=1e-5,
atol=1e-5)
np.testing.assert_allclose(ga[Interval('chr2', 100, 101)],
np.asarray([[[0.706320670013903]]]),
rtol=1e-5,
atol=1e-5)
