def test_normalize_norm_range_h5_cool_equal(capsys):
outfile_one = NamedTemporaryFile(suffix='.cool', delete=False)
outfile_one.close()
outfile_two = NamedTemporaryFile(suffix='.h5', delete=False)
outfile_two.close()
args = "--matrices {} --normalize norm_range -o {}".format(
matrix_one_cool, outfile_one.name).split()
hicNormalize.main(args)
args = "--matrices {} --normalize norm_range -o {}".format(
matrix_one_h5, outfile_two.name).split()
hicNormalize.main(args)
test_one = hm.hiCMatrix(ROOT + "/norm_range_one.cool")
test_two = hm.hiCMatrix(ROOT + "/norm_range_one.h5")
new_one = hm.hiCMatrix(outfile_one.name)
new_two = hm.hiCMatrix(outfile_two.name)
nt.assert_equal(test_one.matrix.data, new_one.matrix.data)
nt.assert_equal(test_one.cut_intervals, new_one.cut_intervals)
nt.assert_equal(test_two.matrix.data, new_two.matrix.data)
nt.assert_equal(test_two.cut_intervals, new_two.cut_intervals)
nt.assert_equal(new_one.matrix.data, new_two.matrix.data)
nt.assert_equal(len(new_one.cut_intervals), len(new_two.cut_intervals))
os.unlink(outfile_one.name)
os.unlink(outfile_two.name)
def test_normalize_smallest_cool(capsys):
outfile_one = NamedTemporaryFile(suffix='.cool', delete=False)
outfile_one.close()
outfile_two = NamedTemporaryFile(suffix='.cool', delete=False)
outfile_two.close()
args = "--matrices {} {} --normalize smallest -o {} {}".format(
matrix_one_cool, matrix_two_cool, outfile_one.name,
outfile_two.name).split()
hicNormalize.main(args)
test_one = hm.hiCMatrix(ROOT + "/smallest_one.cool")
test_two = hm.hiCMatrix(ROOT + "/smallest_two.cool")
new_one = hm.hiCMatrix(outfile_one.name)
new_two = hm.hiCMatrix(outfile_two.name)
nt.assert_equal(test_one.matrix.data, new_one.matrix.data)
nt.assert_equal(test_one.cut_intervals, new_one.cut_intervals)
nt.assert_equal(test_two.matrix.data, new_two.matrix.data)
nt.assert_equal(test_two.cut_intervals, new_two.cut_intervals)
os.unlink(outfile_one.name)
os.unlink(outfile_two.name)
def test_normalize_multiplicative_h5_cool(capsys):
outfile_one = NamedTemporaryFile(suffix='.cool', delete=False)
outfile_one.close()
args = "--matrices {} --normalize multiplicative --multiplicativeValue {} -o {}".format(
matrix_one_cool, 2, outfile_one.name).split()
hicNormalize.main(args)
test_one = hm.hiCMatrix(ROOT + "/small_test_matrix_scaled_by_2.cool")
new_one = hm.hiCMatrix(outfile_one.name)
nt.assert_equal(test_one.matrix.data, new_one.matrix.data)
nt.assert_equal(test_one.cut_intervals, new_one.cut_intervals)
os.unlink(outfile_one.name)