def test_cload_custom_tempdir(bins_path, pairs_path):
for temp_dir in [op.join(testdir, 'data'), '-']:
cload_pairs.callback(
bins_path,
pairs_path,
testcool_path,
metadata=None,
assembly='toy',
chunksize=10,
zero_based=False,
comment_char='#',
input_copy_status='unique',
no_symmetric_upper=False,
field=(),
temp_dir=temp_dir,
no_delete_temp=False,
storage_options=None,
no_count=True,
max_merge=200,
chrom1=1,
pos1=2,
chrom2=3,
pos2=4,
)
pixels = cooler.Cooler(testcool_path).pixels()[:]
assert 'count' in pixels.columns and types.is_integer_dtype(
pixels.dtypes['count'])
def test_cload_field(bins_path, pairs_path):
kwargs = dict(
metadata=None,
assembly='toy',
chunksize=10,
zero_based=False,
comment_char='#',
input_copy_status='unique',
no_symmetric_upper=False,
temp_dir=None,
no_delete_temp=False,
storage_options=None,
no_count=True,
max_merge=200,
chrom1=1,
pos1=2,
chrom2=3,
pos2=4,
)
cload_pairs.callback(bins_path,
pairs_path,
testcool_path,
field=('score=7:dtype=float', ),
**kwargs)
pixels = cooler.Cooler(testcool_path).pixels()[:]
assert 'count' in pixels.columns and types.is_integer_dtype(
pixels.dtypes['count'])
assert 'score' in pixels.columns and types.is_float_dtype(
pixels.dtypes['score'])
def test_cload_custom_tempdir(bins_path, pairs_path):
for temp_dir in [op.join(testdir, "data"), "-"]:
cload_pairs.callback(
bins_path,
pairs_path,
testcool_path,
metadata=None,
assembly="toy",
chunksize=10,
zero_based=False,
comment_char="#",
input_copy_status="unique",
no_symmetric_upper=False,
field=(),
temp_dir=temp_dir,
no_delete_temp=False,
storage_options=None,
no_count=True,
max_merge=200,
chrom1=2,
pos1=3,
chrom2=4,
pos2=5,
)
pixels = cooler.Cooler(testcool_path).pixels()[:]
assert "count" in pixels.columns and types.is_integer_dtype(
pixels.dtypes["count"])
def test_cload_pairs(bins_path, pairs_path, ref_path):
kwargs = dict(
metadata=None,
assembly='hg19',
chunksize=int(15e6),
zero_based=False,
comment_char='#',
input_copy_status='unique',
no_symmetric_upper=False,
field=(),
temp_dir=None,
no_delete_temp=False,
storage_options=None,
no_count=False,
max_merge=200,
chrom1=1,
pos1=2,
chrom2=3,
pos2=4,
)
cload_pairs.callback(bins_path, pairs_path, testcool_path, **kwargs)
with h5py.File(testcool_path, 'r') as f1, \
h5py.File(ref_path, 'r') as f2:
assert np.all(f1['pixels/bin1_id'][:] == f2['pixels/bin1_id'][:])
assert np.all(f1['pixels/bin2_id'][:] == f2['pixels/bin2_id'][:])
assert np.all(f1['pixels/count'][:] == f2['pixels/count'][:])
try:
os.remove(testcool_path)
except OSError:
pass
def test_cload_field(bins_path, pairs_path):
kwargs = dict(
metadata=None,
assembly="toy",
chunksize=10,
zero_based=False,
comment_char="#",
input_copy_status="unique",
no_symmetric_upper=False,
temp_dir=None,
no_delete_temp=False,
storage_options=None,
no_count=True,
max_merge=200,
chrom1=2,
pos1=3,
chrom2=4,
pos2=5,
)
cload_pairs.callback(bins_path,
pairs_path,
testcool_path,
field=("score=8:dtype=float", ),
**kwargs)
pixels = cooler.Cooler(testcool_path).pixels()[:]
assert "count" in pixels.columns and types.is_integer_dtype(
pixels.dtypes["count"])
assert "score" in pixels.columns and types.is_float_dtype(
pixels.dtypes["score"])
