def test_regular_mode_threads():
output_folder = mkdtemp(prefix="output_")
args = "--interactionFile {} {} --targetFile {} --outFileNameSuffix {} \
--outputFolder {} -t {}".format(
ROOT +
'chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt',
ROOT +
'chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt ',
ROOT +
'chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt',
'aggregated.txt', output_folder, 10).split()
chicAggregateStatistic.main(args)
assert are_files_equal(
ROOT +
"chicAggregateStatistic/regular_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt",
output_folder +
'/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt')
assert are_files_equal(
ROOT +
"chicAggregateStatistic/regular_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt",
output_folder +
'/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt')
assert set(os.listdir(ROOT +
"chicAggregateStatistic/regular_mode/")) == set(
os.listdir(output_folder))
def test_target_list():
outfile_aggregate = NamedTemporaryFile(suffix='.hdf5', delete=False)
outfile_aggregate.close()
args = "--interactionFile {} --targetFile {} --outFileName {} \
-t {}".format(ROOT + 'chicViewpoint/two_matrices.hdf5',
ROOT + 'chicAggregateStatistic/target_list.bed',
outfile_aggregate.name, 10).split()
chicAggregateStatistic.main(args)
aggregateFileH5Object = h5py.File(outfile_aggregate.name, 'r')
assert 'FL-E13-5_chr1_MB-E10-5_chr1' in aggregateFileH5Object
assert 'FL-E13-5_chr1' in aggregateFileH5Object[
'FL-E13-5_chr1_MB-E10-5_chr1']
assert 'MB-E10-5_chr1' in aggregateFileH5Object[
'FL-E13-5_chr1_MB-E10-5_chr1']
assert 'genes' in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1'][
'FL-E13-5_chr1']
assert 'genes' in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1'][
'MB-E10-5_chr1']
assert len(aggregateFileH5Object) == 1
assert aggregateFileH5Object.attrs['type'] == 'aggregate'
for chromosome in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1'][
'FL-E13-5_chr1']:
assert len(aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']
['FL-E13-5_chr1'][chromosome]) == 3
for gene in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1'][
'FL-E13-5_chr1'][chromosome]:
assert len(aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']
['FL-E13-5_chr1'][chromosome][gene]) == 7
for data in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1'][
'FL-E13-5_chr1'][chromosome][gene]:
assert data in [
'chromosome', 'end_list', 'gene_name', 'raw_target_list',
'relative_distance_list', 'start_list',
'sum_of_interactions'
]
for chromosome in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1'][
'MB-E10-5_chr1']:
assert len(aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']
['MB-E10-5_chr1'][chromosome]) == 3
for gene in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1'][
'MB-E10-5_chr1'][chromosome]:
assert len(aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1']
['MB-E10-5_chr1'][chromosome][gene]) == 7
for data in aggregateFileH5Object['FL-E13-5_chr1_MB-E10-5_chr1'][
'MB-E10-5_chr1'][chromosome][gene]:
assert data in [
'chromosome', 'end_list', 'gene_name', 'raw_target_list',
'relative_distance_list', 'start_list',
'sum_of_interactions'
]
aggregateFileH5Object.close()
def test_batch_mode():
outfile = NamedTemporaryFile(suffix='.txt', delete=False)
output_folder = mkdtemp(prefix="output_")
outfile.close()
args = "--interactionFile {} --targetFile {} --outFileNameSuffix {} \
--outputFolder {} -iff {} -tff {} -w {} -bm -t {}".format(
ROOT + 'chicViewpoint/fileNames_two_matrices.txt',
ROOT + 'chicSignificantInteractions/output_5_target_list.txt',
'aggregated.txt', output_folder, ROOT + 'chicViewpoint/output_1',
ROOT + 'chicSignificantInteractions/output_5_target', outfile.name,
1).split()
chicAggregateStatistic.main(args)
assert are_files_equal(
ROOT + "chicAggregateStatistic/batch_mode_file_names.txt",
outfile.name)
assert are_files_equal(
ROOT +
"chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt",
output_folder +
'/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt')
assert are_files_equal(
ROOT +
"chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt",
output_folder +
'/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt')
assert are_files_equal(
ROOT +
"chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt",
output_folder +
'/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt')
assert are_files_equal(
ROOT +
"chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt",
output_folder +
'/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt')
assert are_files_equal(
ROOT +
"chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt",
output_folder +
'/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt')
assert are_files_equal(
ROOT +
"chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt",
output_folder +
'/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt')
assert set(os.listdir(ROOT + "chicAggregateStatistic/batch_mode/")) == set(
os.listdir(output_folder))