def test_loose_pValue_multiple_interaction_files():
outfile = NamedTemporaryFile(suffix='.bed', delete=False)
output_folder = mkdtemp(prefix="output_")
output_folder_target = mkdtemp(prefix="output_target_")
outfile.close()
args = "--interactionFile {} {} --backgroundModelFile {} --range {} {} -suffix {} --outputFolder {} --xFoldBackground {} --pValue {} --targetFolder {} -csn 1".format(
ROOT +
'chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed',
ROOT +
'chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed',
ROOT + 'background.bed', 200000, 200000, 'output_significant.bed',
output_folder, 1.5, 0.2, output_folder_target).split()
chicSignificantInteractions.main(args)
assert are_files_equal(
ROOT +
"chicSignificantInteractions/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed",
output_folder +
'/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed')
assert are_files_equal(
ROOT +
"chicSignificantInteractions/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed",
output_folder +
'/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed')
assert set(os.listdir(ROOT +
"chicSignificantInteractions/output_3/")) == set(
os.listdir(output_folder))
assert set(
os.listdir(ROOT +
"chicSignificantInteractions/output_3_target/")) == set(
os.listdir(output_folder_target))
def test_loose_pValue_one_interaction_file_threshold_file():
outfile = NamedTemporaryFile(suffix='.txt', delete=False)
output_folder = mkdtemp(prefix="output_")
output_folder_target = mkdtemp(prefix="output_target_")
outfile.close()
args = "--interactionFile {} --backgroundModelFile {} --range {} {} -suffix {} --outputFolder {} --loosePValue {} --pValue {} --targetFolder {} -t {}".format(
ROOT +
'chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt',
ROOT + 'background.txt', 200000, 200000, 'output_significant.txt',
output_folder, ROOT + 'thresholdFile_loose_pValue.txt',
ROOT + 'thresholdFile_pValue.txt', output_folder_target, 1).split()
chicSignificantInteractions.main(args)
assert are_files_equal(
ROOT +
"chicSignificantInteractions/output_2/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt",
output_folder +
'/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt')
assert set(os.listdir(ROOT +
"chicSignificantInteractions/output_2/")) == set(
os.listdir(output_folder))
assert set(
os.listdir(ROOT +
"chicSignificantInteractions/output_2_target/")) == set(
os.listdir(output_folder_target))
def test_batchMode_xFold_csn_1_threshold_file():
outfile = NamedTemporaryFile(suffix='.txt', delete=False)
outfile_target_list = NamedTemporaryFile(suffix='.txt', delete=False)
outfile_significant_files_list = NamedTemporaryFile(suffix='.txt',
delete=False)
output_folder = mkdtemp(prefix="output_")
output_folder_target = mkdtemp(prefix="output_target_")
outfile.close()
args = "--interactionFile {} --interactionFileFolder {} --backgroundModelFile {} --range {} {} \
-suffix {} --outputFolder {} --xFoldBackground {} --pValue {} --targetFolder {} --writeFileNamesToFile {} --targetFileList {} -bm -csn 1 -t {}".format(
ROOT + 'chicViewpoint/fileNames_one_matrix.txt',
ROOT + 'chicViewpoint/output_2', ROOT + 'background.txt', 200000,
200000, 'output_significant.txt', output_folder,
ROOT + 'thresholdFile_xfold.txt', ROOT + 'thresholdFile_pValue.txt',
output_folder_target, outfile_significant_files_list.name,
outfile_target_list.name, 1).split()
chicSignificantInteractions.main(args)
assert are_files_equal(
ROOT +
"chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt",
output_folder +
'/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt')
assert are_files_equal(
ROOT +
"chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt",
output_folder +
'/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt')
assert are_files_equal(
ROOT +
"chicSignificantInteractions/output_4/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt",
output_folder +
'/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt')
assert are_files_equal(
ROOT + "chicSignificantInteractions/output_4_target_list.txt",
outfile_target_list.name)
assert are_files_equal(
ROOT + "chicSignificantInteractions/output_4_significant_files.txt",
outfile_significant_files_list.name)
assert set(os.listdir(ROOT +
"chicSignificantInteractions/output_4/")) == set(
os.listdir(output_folder))
assert set(
os.listdir(ROOT +
"chicSignificantInteractions/output_4_target/")) == set(
os.listdir(output_folder_target))
def test_batchMode_loose_pValue_csn_2():
outfile = NamedTemporaryFile(suffix='.bed', delete=False)
outfile_target_list = NamedTemporaryFile(suffix='.txt', delete=False)
outfile_significant_files_list = NamedTemporaryFile(suffix='.txt',
delete=False)
output_folder = mkdtemp(prefix="output_")
output_folder_target = mkdtemp(prefix="output_target_")
outfile.close()
args = "--interactionFile {} --interactionFileFolder {} --backgroundModelFile {} --range {} {} \
-suffix {} --outputFolder {} --loosePValue {} --pValue {} --targetFolder {} --writeFileNamesToFile {} --targetFileList {} -bm -csn 2 ".format(
ROOT + 'chicViewpoint/fileNames_two_matrices.txt',
ROOT + 'chicViewpoint/output_1', ROOT + 'background.bed', 200000,
200000, 'output_significant.bed', output_folder, 0.5, 0.2,
output_folder_target, outfile_significant_files_list.name,
outfile_target_list.name).split()
chicSignificantInteractions.main(args)
assert are_files_equal(
ROOT +
"chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed",
output_folder +
'/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed')
assert are_files_equal(
ROOT +
"chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed",
output_folder +
'/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed')
assert are_files_equal(
ROOT +
"chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed",
output_folder +
'/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed')
assert are_files_equal(
ROOT +
"chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed",
output_folder +
'/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed')
assert are_files_equal(
ROOT +
"chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed",
output_folder +
'/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed')
assert are_files_equal(
ROOT +
"chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed",
output_folder +
'/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed')
assert are_files_equal(
ROOT +
"chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.bed",
output_folder_target +
'/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.bed',
skip=4)
assert are_files_equal(
ROOT +
"chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.bed",
output_folder_target +
'/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.bed',
skip=4)
assert are_files_equal(
ROOT +
"chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.bed",
output_folder_target +
'/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.bed',
skip=4)
assert are_files_equal(
ROOT + "chicSignificantInteractions/output_5_target_list.txt",
outfile_target_list.name)
assert are_files_equal(
ROOT + "chicSignificantInteractions/output_5_significant_files.txt",
outfile_significant_files_list.name)
assert set(os.listdir(ROOT +
"chicSignificantInteractions/output_5/")) == set(
os.listdir(output_folder))
assert set(
os.listdir(ROOT +
"chicSignificantInteractions/output_5_target/")) == set(
os.listdir(output_folder_target))
def test_xFold():
outfile_significant = NamedTemporaryFile(suffix='.hdf5', delete=False)
outfile_target = NamedTemporaryFile(suffix='.hdf5', delete=False)
# output_folder = mkdtemp(prefix="output_")
# output_folder_target = mkdtemp(prefix="output_target_")
outfile_significant.close()
outfile_target.close()
args = "--interactionFile {} --backgroundModelFile {} --range {} {} --outFileNameSignificant {} --outFileNameTarget {} --xFoldBackground {} --pValue {} -t {} --combinationMode dual".format(
ROOT + 'chicViewpoint/two_matrices.hdf5', ROOT + 'background.txt',
200000, 200000, outfile_significant.name, outfile_target.name, 1.5,
0.2, 1).split()
chicSignificantInteractions.main(args)
significantFileH5Object = h5py.File(outfile_significant.name, 'r')
assert 'FL-E13-5_chr1' in significantFileH5Object
assert 'MB-E10-5_chr1' in significantFileH5Object
assert 'genes' in significantFileH5Object['FL-E13-5_chr1']
assert 'genes' in significantFileH5Object['MB-E10-5_chr1']
assert len(significantFileH5Object) == 2
assert significantFileH5Object.attrs['type'] == 'significant'
assert len(significantFileH5Object.attrs['range']) == 2
assert significantFileH5Object.attrs['range'][0] == 200000
assert significantFileH5Object.attrs['range'][1] == 200000
# assert significantFileH5Object.attrs['averageContactBin'] == 5
assert significantFileH5Object.attrs['fixateRange'] == 500000
assert significantFileH5Object.attrs['mode_preselection'] == 'xfold'
assert significantFileH5Object.attrs['mode_preselection_value'] == 1.5
assert significantFileH5Object.attrs['pvalue'] == 0.2
assert significantFileH5Object.attrs['combinationMode'] == 'dual'
assert significantFileH5Object.attrs['truncateZeroPvalues'] == False
assert significantFileH5Object.attrs['peakInteractionsThreshold'] == 5
for chromosome in significantFileH5Object['FL-E13-5_chr1']:
assert len(significantFileH5Object['FL-E13-5_chr1'][chromosome]) == 3
for gene in significantFileH5Object['FL-E13-5_chr1'][chromosome]:
assert len(significantFileH5Object['FL-E13-5_chr1'][chromosome]
[gene]) == 12
for data in significantFileH5Object['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'
]
for chromosome in significantFileH5Object['MB-E10-5_chr1']:
assert len(significantFileH5Object['MB-E10-5_chr1'][chromosome]) == 3
for gene in significantFileH5Object['MB-E10-5_chr1'][chromosome]:
assert len(significantFileH5Object['MB-E10-5_chr1'][chromosome]
[gene]) == 12
for data in significantFileH5Object['MB-E10-5_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'
]
significantFileH5Object.close()
targetFileH5Object = h5py.File(outfile_target.name, 'r')
assert 'FL-E13-5_chr1' in targetFileH5Object
assert 'MB-E10-5_chr1' in targetFileH5Object['FL-E13-5_chr1']
# assert 'genes' in targetFileH5Object['FL-E13-5_chr1']
assert len(targetFileH5Object) == 1
assert len(targetFileH5Object['FL-E13-5_chr1']) == 1
assert targetFileH5Object.attrs['type'] == 'target'
assert len(targetFileH5Object.attrs['range']) == 2
assert targetFileH5Object.attrs['range'][0] == 200000
assert targetFileH5Object.attrs['range'][1] == 200000
# assert targetFileH5Object.attrs['averageContactBin'] == 5
assert targetFileH5Object.attrs['fixateRange'] == 500000
assert targetFileH5Object.attrs['mode_preselection'] == 'xfold'
assert targetFileH5Object.attrs['mode_preselection_value'] == 1.5
assert targetFileH5Object.attrs['pvalue'] == 0.2
assert targetFileH5Object.attrs['combinationMode'] == 'dual'
assert targetFileH5Object.attrs['truncateZeroPvalues'] == False
assert targetFileH5Object.attrs['peakInteractionsThreshold'] == 5
for matrix in targetFileH5Object['FL-E13-5_chr1']:
assert len(targetFileH5Object['FL-E13-5_chr1'][matrix]) == 2
for chromosome in targetFileH5Object['FL-E13-5_chr1'][matrix]:
assert len(
targetFileH5Object['FL-E13-5_chr1'][matrix][chromosome]) == 3
for gene in targetFileH5Object['FL-E13-5_chr1'][matrix][chromosome]:
assert len(targetFileH5Object['FL-E13-5_chr1'][matrix][chromosome]
[gene]) == 5
for data in targetFileH5Object['FL-E13-5_chr1'][matrix][
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'
]
targetFileH5Object.close()