def test_hicConvertFormat_h5_to_ginteractions():
outfile = NamedTemporaryFile(suffix='.ginteractions', delete=False)
outfile.close()
args = "--matrices {} --outFileName {} --inputFormat h5 --outputFormat ginteractions ".format(
original_matrix_h5, outfile.name).split()
hicConvertFormat.main(args)
def test_trivial_run(
matrices,
outputFormat,
resolutions,
):
"""
Test for all commandline arguments.
Options for cool input format are testet seperately.
"""
from pathlib import Path
# get suffix of input matrix without the dot
inputFormat = Path(matrices).suffix[1:]
# create file corresponding to output format
outFileName = NamedTemporaryFile(suffix=".{}".format(outputFormat),
delete=True)
args = "--matrices {} --outFileName {} --inputFormat {} --outputFormat {} {}".format(
matrices,
outFileName.name,
inputFormat,
outputFormat,
resolutions,
).split()
hicConvertFormat.main(args)
def test_hicConvertFormat_h5_to_mcool():
outfile = NamedTemporaryFile(suffix='.cool', delete=False)
outfile.close()
args = "--matrices {} --outFileName {} --inputFormat h5 --outputFormat mcool -r 10000 100000 200000 ".format(original_matrix_h5, outfile.name).split()
hicConvertFormat.main(args)
new1 = hm.hiCMatrix(outfile.name + '::/resolutions/10000') # noqa: F841
new2 = hm.hiCMatrix(outfile.name + '::/resolutions/100000') # noqa: F841
new3 = hm.hiCMatrix(outfile.name + '::/resolutions/200000') # noqa: F841
def test_hicConvertFormat_h5_to_cool():
# original_matrix = ''
outfile = NamedTemporaryFile(suffix='.cool', delete=False)
outfile.close()
args = "--matrices {} --outFileName {} --inputFormat h5 --outputFormat cool".format(original_matrix_h5, outfile.name).split()
hicConvertFormat.main(args)
test = hm.hiCMatrix(original_matrix_cool)
# print(outfile.name)
new = hm.hiCMatrix(outfile.name)
nt.assert_array_almost_equal(test.matrix.data, new.matrix.data, decimal=DELTA_DECIMAL)
def test_hicConvertFormat_h5_to_cool_enforce_integer():
outfile = NamedTemporaryFile(suffix='.cool', delete=False)
outfile.close()
args = "--matrices {} --outFileName {} --inputFormat h5 --outputFormat cool ".format(
original_matrix_h5, outfile.name).split()
hicConvertFormat.main(args)
test = hm.hiCMatrix(original_matrix_cool)
new = hm.hiCMatrix(outfile.name)
nt.assert_array_almost_equal(test.matrix.data, new.matrix.data, decimal=0)
assert issubclass(test.matrix.data.dtype.type, np.integer)
def test_trivial_functionality(
matrices,
outputFormat,
resolutions,
):
"""
Test for all commandline arguments.
Options for cool input format are testet seperately.
"""
from pathlib import Path
# get suffix of input matrix without the dot
inputFormat = Path(matrices).suffix[1:]
# create file corresponding to output format
outFileName = NamedTemporaryFile(suffix=".{}".format(outputFormat),
delete=True)
outFileName.close()
args = "--matrices {} --outFileName {} --inputFormat {} --outputFormat {} {}".format(
matrices,
outFileName.name,
inputFormat,
outputFormat,
resolutions,
).split()
hicConvertFormat.main(args)
test = hm.hiCMatrix(matrices)
new = hm.hiCMatrix(outFileName.name)
nt.assert_array_almost_equal(test.matrix.data,
new.matrix.data,
decimal=DELTA_DECIMAL)
nt.assert_equal(len(new.cut_intervals), len(test.cut_intervals))
cut_interval_new_ = []
cut_interval_test_ = []
for x in new.cut_intervals:
cut_interval_new_.append(x[:3])
for x in test.cut_intervals:
cut_interval_test_.append(x[:3])
nt.assert_equal(cut_interval_new_, cut_interval_test_)
os.unlink(outFileName.name)
def test_hicConvertFormat_hicpro_to_cool():
outfile = NamedTemporaryFile(suffix='.cool', delete=False)
outfile.close()
hicprofile = ROOT + '/test_matrix.hicpro'
bedfile = ROOT + '/test_matrix.bed'
args = "--matrices {} --outFileName {} --inputFormat hicpro --outputFormat cool --bedFileHicpro {}".format(hicprofile, outfile.name, bedfile).split()
hicConvertFormat.main(args)
# test = hm.hiCMatrix(original_matrix_cool)
# print(outfile.name)
new = hm.hiCMatrix(outfile.name)
matrixFileHandlerInput = MatrixFileHandler(pFileType='hicpro', pMatrixFile=hicprofile,
pBedFileHicPro=bedfile)
_matrix, cut_intervals, nan_bins, \
distance_counts, correction_factors = matrixFileHandlerInput.load()
new.matrix = triu(new.matrix)
nt.assert_array_almost_equal(new.matrix.data, _matrix.data, decimal=0)
def test_hicConvertFormat_h5_to_homer():
outfile = NamedTemporaryFile(suffix='.homer', delete=False)
outfile.close()
args = "--matrices {} --outFileName {} --inputFormat cool --outputFormat homer ".format(original_matrix_cool_chr4, outfile.name).split()
hicConvertFormat.main(args)
test = hm.hiCMatrix(original_matrix_cool_chr4)
f = gzip.open(outfile.name, 'rb')
file_content = f.read()
outfile2 = NamedTemporaryFile(suffix='.homer', delete=False)
outfile2.close()
with open(outfile2.name, 'wb') as matrix_file:
matrix_file.write(file_content)
matrixFileHandlerInput = MatrixFileHandler(pFileType='homer', pMatrixFile=outfile2.name)
_matrix, cut_intervals, nan_bins, \
distance_counts, correction_factors = matrixFileHandlerInput.load()
nt.assert_array_almost_equal(test.matrix.data, _matrix.data, decimal=0)
def test_cool_specific_trivial_run(
matrices,
outputFormat,
correction_name,
correction_division,
store_applied_correction,
chromosome,
enforce_integer,
load_raw_values,
):
"""
Cool input format supports some specific options like correction_name, correction_division...
Therefore, cool input format is explicitly tested in a single test function.
"""
from pathlib import Path
# get suffix of input matrix without the dot
inputFormat = Path(matrices).suffix[1:]
# create file corresponding to output format
outFileName = NamedTemporaryFile(
suffix="test_ConvertFormat_trivial_run_cool.{}".format(outputFormat),
delete=False)
outFileName.close()
args = "--matrices {} --outFileName {} --outputFormat {} --inputFormat {} --correction_name {} {} {} --chromosome {} {} {}".format(
matrices,
outFileName.name,
outputFormat,
inputFormat,
correction_name,
correction_division,
store_applied_correction,
chromosome,
enforce_integer,
load_raw_values,
).split()
hicConvertFormat.main(args)
