def test_interaction_bigwig_all():
outfile = NamedTemporaryFile(suffix='.tar.gz', delete=False)
outfile.close()
args = "-f {} -o {} -om {} -oft {} --range {} {} --backgroundModelFile {} --chromosomeSizes {}".format(
ROOT + 'chicViewpoint/two_matrices.hdf5', outfile.name, 'all',
'bigwig', 20000, 200000, ROOT + 'background.txt',
ROOT + 'hg19.chrom.sizes').split()
chicExportData.main(args)
file_obj_new = tarfile.open(outfile.name, "r")
namelist = file_obj_new.getnames()
assert len(namelist) == 12
output_folder_new = mkdtemp(prefix="output_")
output_folder_test_data = mkdtemp(prefix="output_")
file_obj_new.extractall(output_folder_new)
file_obj_test_data = tarfile.open(
ROOT + 'chicExportData/interaction_all_bigwig.tar.gz', "r")
file_obj_test_data.extractall(output_folder_test_data)
namelist = file_obj_test_data.getnames()
assert len(namelist) == 12
files_new = os.listdir(output_folder_new)
files_test_data = os.listdir(output_folder_test_data)
files_new = sorted(files_new)
files_test_data = sorted(files_test_data)
for file_new, file_test_data in zip(files_new, files_test_data):
assert are_files_equal_bigwig(
output_folder_new + '/' + file_new,
output_folder_test_data + '/' + file_test_data, ['chr1'])
def test_interactions_all():
outfile = NamedTemporaryFile(suffix='.tar.gz', delete=False)
outfile.close()
args = "-f {} -o {} -om {}".format(
ROOT + 'chicViewpoint/two_matrices.hdf5', outfile.name, 'all').split()
chicExportData.main(args)
file_obj_new = tarfile.open(outfile.name, "r")
namelist = file_obj_new.getnames()
assert len(namelist) == 6
output_folder_new = mkdtemp(prefix="output_")
output_folder_test_data = mkdtemp(prefix="output_")
file_obj_new.extractall(output_folder_new)
file_obj_test_data = tarfile.open(
ROOT + 'chicExportData/interaction_all_txt.tar.gz', "r")
file_obj_test_data.extractall(output_folder_test_data)
files_new = os.listdir(output_folder_new)
files_test_data = os.listdir(output_folder_test_data)
files_new = sorted(files_new)
files_test_data = sorted(files_test_data)
for file_new, file_test_data in zip(files_new, files_test_data):
assert are_files_equal(output_folder_new + '/' + file_new,
output_folder_test_data + '/' + file_test_data,
skip=1)
def test_target_one_gene_bigwig_fail():
outfile = NamedTemporaryFile(suffix='.tar.gz', delete=False)
outfile.close()
args = "-f {} -o {} -om {} -omn {} -oft {}".format(
ROOT + 'chicSignificantInteractions/targetFile_dual.hdf5',
outfile.name, 'geneName', 'Eya1', 'bigwig').split()
chicExportData.main(args)
def test_interaction_bigwig_fail_range_background():
outfile = NamedTemporaryFile(suffix='.tar.gz', delete=False)
outfile.close()
args = "-f {} -o {} -om {} -oft {} --range {} {} --backgroundModelFile {}".format(
ROOT + 'chicViewpoint/two_matrices.hdf5', outfile.name, 'all',
'bigwig', 20000, 200000, 'background.txt').split()
chicExportData.main(args)
def test_interaction_bigwig_fail():
outfile = NamedTemporaryFile(suffix='.tar.gz', delete=False)
outfile.close()
args = "-f {} -o {} -om {} -oft {}".format(
ROOT + 'chicViewpoint/two_matrices.hdf5', outfile.name, 'all',
'bigwig').split()
chicExportData.main(args)
def test_target_oneGene():
output_folder_new = mkdtemp(prefix="output")
args = "-f {} -o {} -om {} -omn Eya1".format(
ROOT + 'chicSignificantInteractions/targetFile_dual.hdf5',
output_folder_new, 'geneName').split()
chicExportData.main(args)
files_new = os.listdir(output_folder_new)
files_test_data = ['FL-E13-5_chr1_MB-E10-5_chr1_genes_Eya1_target.txt']
files_new = sorted(files_new)
files_test_data = sorted(files_test_data)
for file_new, file_test_data in zip(files_new, files_test_data):
assert are_files_equal(output_folder_new + '/' + file_new,
ROOT + '/chicExportData/' + file_test_data,
skip=1)
def test_aggregate_oneGene():
output_folder_new = mkdtemp(prefix="output")
args = "-f {} -o {} -om {} -omn Eya1".format(
ROOT + 'chicAggregateStatistic/aggregate.hdf5', output_folder_new,
'geneName').split()
chicExportData.main(args)
files_new = os.listdir(output_folder_new)
files_test_data = [
'FL-E13-5_chr1_MB-E10-5_chr1_FL-E13-5_chr1_genes_Eya1_aggregate.txt',
'FL-E13-5_chr1_MB-E10-5_chr1_MB-E10-5_chr1_genes_Eya1_aggregate.txt'
]
files_new = sorted(files_new)
files_test_data = sorted(files_test_data)
for file_new, file_test_data in zip(files_new, files_test_data):
assert are_files_equal(output_folder_new + '/' + file_new,
ROOT + '/chicExportData/' + file_test_data,
skip=1)
def test_differential_one_gene():
output_folder_new = mkdtemp(prefix="output")
args = "-f {} -o {} -om {} -omn Eya1".format(
ROOT + 'chicDifferentialTest/differential.hdf5', output_folder_new,
'geneName').split()
chicExportData.main(args)
files_new = os.listdir(output_folder_new)
files_test_data = [
'FL-E13-5_chr1_MB-E10-5_chr1_genes_Eya1_accepted_differential.txt',
'FL-E13-5_chr1_MB-E10-5_chr1_genes_Eya1_all_differential.txt',
'FL-E13-5_chr1_MB-E10-5_chr1_genes_Eya1_rejected_differential.txt'
]
files_new = sorted(files_new)
files_test_data = sorted(files_test_data)
for file_new, file_test_data in zip(files_new, files_test_data):
assert are_files_equal(output_folder_new + '/' + file_new,
ROOT + '/chicExportData/' + file_test_data,
skip=1)
def test_interaction_bigwig_oneGene():
output_folder_new = mkdtemp(prefix="output")
args = "-f {} -o {} -om {} -omn {} -oft {} --range {} {} --backgroundModelFile {} --chromosomeSizes {}".format(
ROOT + 'chicViewpoint/two_matrices.hdf5',
output_folder_new + '/data.tar.gz', 'geneName', 'Eya1', 'bigwig',
20000, 200000, ROOT + 'background.txt',
ROOT + 'hg19.chrom.sizes').split()
chicExportData.main(args)
files_new = os.listdir(output_folder_new)
assert len(files_new) == 4
name_list_oneGene_bigWig = [
"background_FL-E13-5_chr1_genes_Eya1_interactions.bigwig",
'background_MB-E10-5_chr1_genes_Eya1_interactions.bigwig',
'FL-E13-5_chr1_genes_Eya1.bigwig', 'MB-E10-5_chr1_genes_Eya1.bigwig'
]
files_test_data = name_list_oneGene_bigWig
files_new = sorted(files_new)
files_test_data = sorted(files_test_data)
for file_new, file_test_data in zip(files_new, files_test_data):
assert are_files_equal_bigwig(
output_folder_new + '/' + file_new,
ROOT + '/chicExportData/' + file_test_data, ['chr1'])
