def test_one_matrix():
outfile = NamedTemporaryFile(suffix='.hdf5', delete=False)
outfile.close()
args = "--matrices {} --referencePoints {} --backgroundModel {} --range {} {} -o {} -t {}".format(
ROOT + 'FL-E13-5_chr1.cool',
ROOT + 'referencePoints_chicViewpoint.bed', ROOT + 'background.txt',
200000, 200000, outfile.name, 1).split()
chicViewpoint.main(args)
interactionFileH5Object = h5py.File(outfile.name, 'r')
assert 'FL-E13-5_chr1' in interactionFileH5Object
assert len(interactionFileH5Object) == 1
assert 'genes' in interactionFileH5Object['FL-E13-5_chr1']
assert interactionFileH5Object.attrs['type'] == 'interactions'
assert len(interactionFileH5Object.attrs['range']) == 2
assert interactionFileH5Object.attrs['range'][0] == 200000
assert interactionFileH5Object.attrs['range'][1] == 200000
assert interactionFileH5Object.attrs['averageContactBin'] == 5
assert interactionFileH5Object.attrs['fixateRange'] == 500000
for chromosome in interactionFileH5Object['FL-E13-5_chr1']:
assert len(interactionFileH5Object['FL-E13-5_chr1'][chromosome]) == 3
for gene in interactionFileH5Object['FL-E13-5_chr1'][chromosome]:
assert len(interactionFileH5Object['FL-E13-5_chr1'][chromosome]
[gene]) == 12
for data in interactionFileH5Object['FL-E13-5_chr1'][chromosome][
gene]:
assert data in [
'chromosome', 'end_list', 'gene', 'interaction_data_list',
'pvalue', 'raw', 'reference_point_end',
'reference_point_start', 'relative_position_list',
'start_list', 'sum_of_interactions', 'xfold'
]
def test_one_matrix():
outfile = NamedTemporaryFile(suffix='.bed', delete=False)
output_folder = mkdtemp(prefix="output_")
outfile.close()
args = "--matrices {} --referencePoints {} --backgroundModel {} --range {} {} -o {}".format(
ROOT + 'FL-E13-5_chr1.cool',
ROOT + 'referencePoints_chicViewpoint.bed', ROOT + 'background.bed',
200000, 200000, output_folder).split()
chicViewpoint.main(args)
assert are_files_equal(
ROOT +
"chicViewpoint/output_2/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed",
output_folder + '/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed',
skip=4)
assert are_files_equal(
ROOT +
"chicViewpoint/output_2/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed",
output_folder + '/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed',
skip=4)
assert are_files_equal(
ROOT +
"chicViewpoint/output_2/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed",
output_folder + '/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed',
skip=4)
assert set(os.listdir(ROOT + "chicViewpoint/output_2/")) == set(
os.listdir(output_folder))
def test_two_matrices_writeFileName_crash():
outfile = NamedTemporaryFile(suffix='.txt', delete=False)
outfile_name_list = NamedTemporaryFile(suffix='.txt', delete=False)
output_folder = mkdtemp(prefix="output_")
outfile.close()
args = "--matrices {} {} --referencePoints {} --backgroundModel {} --range {} {} -o {} -w {} -t {} --decimalPlaces {}".format(
ROOT + 'FL-E13-5_chr1.cool', ROOT + 'MB-E10-5_chr1.cool',
ROOT + 'referencePoints_chicViewpoint_crash.bed',
ROOT + 'background.txt', 200000, 200000, output_folder,
outfile_name_list.name, 1, 5).split()
chicViewpoint.main(args)
assert are_files_equal(ROOT + "chicViewpoint/fileNames_two_matrices.txt",
outfile_name_list.name)
assert are_files_equal(
ROOT +
"chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt",
output_folder + '/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt',
skip=4)
assert are_files_equal(
ROOT +
"chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt",
output_folder + '/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt',
skip=4)
assert are_files_equal(
ROOT +
"chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt",
output_folder + '/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt',
skip=4)
assert are_files_equal(
ROOT +
"chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt",
output_folder + '/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt',
skip=4)
assert are_files_equal(
ROOT +
"chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt",
output_folder + '/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt',
skip=4)
assert are_files_equal(
ROOT +
"chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt",
output_folder + '/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt',
skip=4)
assert set(os.listdir(ROOT + "chicViewpoint/output_3/")) == set(
os.listdir(output_folder))