def test_regular_mode_chi2():
output_folder = mkdtemp(prefix="output_")
args = "--interactionFile {} {} --alpha {} --statisticTest {} --outputFolder {}\
".format(
ROOT +
'chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed',
ROOT +
'chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed ',
0.5, 'chi2', output_folder).split()
chicDifferentialTest.main(args)
assert are_files_equal(
ROOT +
"chicDifferentialTest/regular_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.bed",
output_folder +
'/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.bed')
assert are_files_equal(
ROOT +
"chicDifferentialTest/regular_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed",
output_folder +
'/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed')
assert are_files_equal(
ROOT +
"chicDifferentialTest/regular_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed",
output_folder +
'/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed')
assert set(os.listdir(ROOT +
"chicDifferentialTest/regular_mode_chi2/")) == set(
os.listdir(output_folder))
def test_regular_mode_chi2():
outfile_differential = NamedTemporaryFile(suffix='.hdf5', delete=False)
outfile_differential.close()
args = "--aggregatedFile {} --alpha {} --statisticTest {} --outFileName {} -t {}\
".format(ROOT + 'chicAggregateStatistic/aggregate.hdf5', 0.5, 'chi2',
outfile_differential.name, 1).split()
chicDifferentialTest.main(args)
differentialFileH5Object = h5py.File(outfile_differential.name, 'r')
assert 'FL-E13-5_chr1' in differentialFileH5Object
assert len(differentialFileH5Object) == 1
assert 'MB-E10-5_chr1' in differentialFileH5Object['FL-E13-5_chr1']
assert 'genes' in differentialFileH5Object['FL-E13-5_chr1'][
'MB-E10-5_chr1']
assert differentialFileH5Object.attrs['type'] == 'differential'
assert differentialFileH5Object.attrs['alpha'] == 0.5
assert differentialFileH5Object.attrs['test'] == 'chi2'
for chromosome in differentialFileH5Object['FL-E13-5_chr1'][
'MB-E10-5_chr1']:
assert len(differentialFileH5Object['FL-E13-5_chr1']['MB-E10-5_chr1']
[chromosome]) == 3
for gene in differentialFileH5Object['FL-E13-5_chr1']['MB-E10-5_chr1'][
chromosome]:
assert len(differentialFileH5Object['FL-E13-5_chr1']
['MB-E10-5_chr1'][chromosome][gene]) == 3
for data in differentialFileH5Object['FL-E13-5_chr1'][
'MB-E10-5_chr1'][chromosome][gene]:
assert len(differentialFileH5Object['FL-E13-5_chr1']
['MB-E10-5_chr1'][chromosome][gene][data]) == 10
for status in differentialFileH5Object['FL-E13-5_chr1'][
'MB-E10-5_chr1'][chromosome][gene][data]:
assert status in [
'chromosome', 'end_list', 'gene', 'pvalue_list',
'raw_target_list_1', 'raw_target_list_2',
'relative_distance_list', 'start_list',
'sum_of_interactions_1', 'sum_of_interactions_2'
]
differentialFileH5Object.close()
def test_batch_mode_fisher_rejected_file():
output_folder = mkdtemp(prefix="output_")
outfile = NamedTemporaryFile(suffix='.txt', delete=False)
args = "--interactionFile {} -iff {} --alpha {} --statisticTest {} --outputFolder {} -bm --rejectedFileNamesToFile {}\
".format(ROOT + 'chicAggregateStatistic/batch_mode_file_names.txt',
ROOT + 'chicAggregateStatistic/batch_mode', 0.5, 'fisher',
output_folder, outfile.name).split()
chicDifferentialTest.main(args)
assert are_files_equal(
ROOT +
"chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.bed",
output_folder +
'/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.bed')
assert are_files_equal(
ROOT +
"chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed",
output_folder +
'/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed')
assert are_files_equal(
ROOT +
"chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed",
output_folder +
'/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed')
assert are_files_equal(
ROOT +
"chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.bed",
output_folder +
'/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.bed'
)
assert are_files_equal(
ROOT +
"chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.bed",
output_folder +
'/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.bed'
)
assert are_files_equal(
ROOT +
"chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.bed",
output_folder +
'/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.bed')
assert are_files_equal(
ROOT +
"chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.bed",
output_folder +
'/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.bed')
assert are_files_equal(
ROOT +
"chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.bed",
output_folder +
'/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.bed')
assert are_files_equal(
ROOT +
"chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.bed",
output_folder +
'/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.bed')
assert are_files_equal(ROOT + "chicDifferentialTest/rejectedFilesList.txt",
outfile.name)
assert set(
os.listdir(ROOT +
"chicDifferentialTest/batch_mode_fisher_outfile/")) == set(
os.listdir(output_folder))
def test_batch_mode_chi2():
output_folder = mkdtemp(prefix="output_")
args = "--interactionFile {} -iff {} --alpha {} --statisticTest {} --outputFolder {} -bm\
".format(ROOT + 'chicAggregateStatistic/batch_mode_file_names.txt',
ROOT + 'chicAggregateStatistic/batch_mode', 0.5, 'chi2',
output_folder).split()
chicDifferentialTest.main(args)
assert are_files_equal(
ROOT +
"chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.bed",
output_folder +
'/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.bed')
assert are_files_equal(
ROOT +
"chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed",
output_folder +
'/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed')
assert are_files_equal(
ROOT +
"chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed",
output_folder +
'/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed')
assert are_files_equal(
ROOT +
"chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.bed",
output_folder +
'/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.bed'
)
assert are_files_equal(
ROOT +
"chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.bed",
output_folder +
'/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.bed'
)
assert are_files_equal(
ROOT +
"chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.bed",
output_folder +
'/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.bed')
assert are_files_equal(
ROOT +
"chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.bed",
output_folder +
'/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.bed')
assert are_files_equal(
ROOT +
"chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.bed",
output_folder +
'/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.bed')
assert are_files_equal(
ROOT +
"chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.bed",
output_folder +
'/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.bed')
assert set(os.listdir(ROOT +
"chicDifferentialTest/batch_mode_chi2/")) == set(
os.listdir(output_folder))