def test_hic_transfer_all():
outfile = NamedTemporaryFile(suffix='all.h5', delete=False)
outfile.close()
args = "--matrix {} --outFileName {} --method all".format(
original_matrix, outfile.name).split()
hicTransform.main(args)
dirname_new = dirname(outfile.name)
basename_new = basename(outfile.name)
# obs_exp
test = hm.hiCMatrix(ROOT + "hicTransform/obs_exp_small_50kb.h5")
new = hm.hiCMatrix(dirname_new + "/obs_exp_" + basename_new)
nt.assert_array_almost_equal(test.matrix.data, new.matrix.data)
os.unlink(dirname_new + "/obs_exp_" + basename_new)
# pearson
test = hm.hiCMatrix(ROOT + "hicTransform/pearson_small_50kb.h5")
new = hm.hiCMatrix(dirname_new + "/pearson_" + basename_new)
nt.assert_array_almost_equal(test.matrix.data, new.matrix.data)
os.unlink(dirname_new + "/pearson_" + basename_new)
# covariance
test = hm.hiCMatrix(ROOT + "hicTransform/covariance_small_50kb.h5")
new = hm.hiCMatrix(dirname_new + "/covariance_" + basename_new)
nt.assert_array_almost_equal(test.matrix.data, new.matrix.data)
os.unlink(dirname_new + "/covariance_" + basename_new)
os.unlink(outfile.name)
def test_hic_transfer_covariance():
outfile = NamedTemporaryFile(suffix='covariance_.h5', delete=False)
outfile.close()
matrix = ROOT + "/hicTransform/pearson_small_50kb.h5"
args = "--matrix {} --outFileName {} --method covariance".format(
matrix, outfile.name).split()
hicTransform.main(args)
test = hm.hiCMatrix(ROOT + "hicTransform/covariance_small_50kb.h5")
new = hm.hiCMatrix(outfile.name)
nt.assert_array_almost_equal(test.matrix.data, new.matrix.data)
os.unlink(outfile.name)
def test_hic_transfer_obs_exp():
outfile = NamedTemporaryFile(suffix='obs_exp_.h5', delete=False)
outfile.close()
args = "--matrix {} --outFileName {} --method obs_exp".format(
original_matrix, outfile.name).split()
hicTransform.main(args)
test = hm.hiCMatrix(ROOT + "hicTransform/obs_exp_small_50kb.h5")
new = hm.hiCMatrix(outfile.name)
nt.assert_array_almost_equal(test.matrix.data, new.matrix.data)
os.unlink(outfile.name)
def test_hic_transfer_covariance_perChromosome():
outfile = NamedTemporaryFile(suffix='covariance_.h5', delete=False)
outfile.close()
args = "--matrix {} --outFileName {} --method covariance --perChromosome".format(
original_matrix, outfile.name).split()
hicTransform.main(args)
test = hm.hiCMatrix(ROOT + "hicTransform/covariance_perChromosome.h5")
new = hm.hiCMatrix(outfile.name)
nt.assert_array_almost_equal(test.matrix.data,
new.matrix.data,
decimal=DELTA_DECIMAL)
os.unlink(outfile.name)
def test_hic_transfer_obs_exp_non_zero():
outfile = NamedTemporaryFile(suffix='obs_exp_.cool', delete=False)
outfile.close()
args = "--matrix {} --outFileName {} --method obs_exp_non_zero".format(
original_matrix_cool, outfile.name).split()
hicTransform.main(args)
test = hm.hiCMatrix(ROOT + "hicTransform/obs_exp_non_zero.cool")
new = hm.hiCMatrix(outfile.name)
nt.assert_array_almost_equal(test.matrix.data,
new.matrix.data,
decimal=DELTA_DECIMAL)
os.unlink(outfile.name)
