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)