def test_two_viewpoints_per_file_batch_mode_significances_differential_pvalue(
):
output_folder = mkdtemp(prefix="output_")
args = "-if {} -iff {} --range {} {} --outputFolder {} -psn {} -bm --differentialTestResult {} -diff {} -si {} -siff {} -p -xf {} -bmf {} -t {}".format(
ROOT + 'chicViewpoint/fileNames_two_matrices.txt',
ROOT + 'chicViewpoint/output_1', 200000, 200000, output_folder, 2,
ROOT + 'chicDifferentialTest/rejectedFilesList.txt',
ROOT + 'chicDifferentialTest/batch_mode_fisher_outfile/',
ROOT + 'chicSignificantInteractions/output_5_significant_files.txt',
ROOT + 'chicSignificantInteractions/output_5/', 1.5,
ROOT + 'background.txt', 1).split()
chicPlotViewpoint.main(args)
res = compare_images(
ROOT +
'chicPlotViewpoint/batchMode/two/Eya1_FL-E13-5_MB-E10-5_chr1_chr1_14300280.png',
output_folder + '/Eya1_FL-E13-5_MB-E10-5_chr1_chr1_14300280.png',
tolerance)
assert res is None, res
res = compare_images(
ROOT +
'chicPlotViewpoint/batchMode/two/Sox17_FL-E13-5_MB-E10-5_chr1_chr1_4487435.png',
output_folder + '/Sox17_FL-E13-5_MB-E10-5_chr1_chr1_4487435.png',
tolerance)
assert res is None, res
res = compare_images(
ROOT +
'chicPlotViewpoint/batchMode/two/Tfap2d_FL-E13-5_MB-E10-5_chr1_chr1_19093103.png',
output_folder + '/Tfap2d_FL-E13-5_MB-E10-5_chr1_chr1_19093103.png',
tolerance)
assert res is None, res
assert set(os.listdir(ROOT + "chicPlotViewpoint/batchMode/two")) == set(
os.listdir(output_folder))
def test_one_viewpoint_per_file_batch_mode():
output_folder = mkdtemp(prefix="output_")
args = "-if {} -iff {} --range {} {} --outputFolder {} -psn {} -bm -t {}".format(
ROOT + 'chicViewpoint/fileNames_one_matrix.txt',
ROOT + 'chicViewpoint/output_4', 200000, 200000, output_folder, 1,
1).split()
chicPlotViewpoint.main(args)
res = compare_images(
ROOT +
'chicPlotViewpoint/batchMode/one/Eya1_FL-E13-5_chr1_chr1_14300280.png',
output_folder + '/Eya1_FL-E13-5_chr1_chr1_14300280.png', tolerance)
assert res is None, res
res = compare_images(
ROOT +
'chicPlotViewpoint/batchMode/one/Sox17_FL-E13-5_chr1_chr1_4487435.png',
output_folder + '/Sox17_FL-E13-5_chr1_chr1_4487435.png', tolerance)
assert res is None, res
res = compare_images(
ROOT +
'chicPlotViewpoint/batchMode/one/Tfap2d_FL-E13-5_chr1_chr1_19093103.png',
output_folder + '/Tfap2d_FL-E13-5_chr1_chr1_19093103.png', tolerance)
assert res is None, res
assert set(os.listdir(ROOT + "chicPlotViewpoint/batchMode/one")) == set(
os.listdir(output_folder))
def test_single_significant_pvalue():
outfile = NamedTemporaryFile(suffix='.tar.gz', delete=False)
outfile.close()
args = "-if {} --range {} {} -o {} -t {} --combinationMode single --backgroundModelFile {} --significantInteractions {} --pValue --plotSignificantInteractions".format(
ROOT + 'chicViewpoint/two_matrices.hdf5', 200000, 200000, outfile.name,
1, ROOT + 'background.txt',
ROOT + 'chicSignificantInteractions/significantInteractions_dual.hdf5'
).split()
chicPlotViewpoint.main(args)
file_obj = tarfile.open(outfile.name, "r")
namelist = file_obj.getnames()
assert len(namelist) == 6
assert 'FL-E13-5_chr1_Eya1.png' in namelist
assert 'MB-E10-5_chr1_Eya1.png' in namelist
assert 'FL-E13-5_chr1_Sox17.png' in namelist
assert 'MB-E10-5_chr1_Sox17.png' in namelist
assert 'FL-E13-5_chr1_Tfap2d.png' in namelist
assert 'MB-E10-5_chr1_Tfap2d.png' in namelist
output_folder = mkdtemp(prefix="output_")
file_obj.extractall(output_folder)
res = compare_images(
ROOT +
'chicPlotViewpoint/background_single_signficant_pvalues/FL-E13-5_chr1_Eya1.png',
output_folder + '/FL-E13-5_chr1_Eya1.png', tolerance)
assert res is None, res
res = compare_images(
ROOT +
'chicPlotViewpoint/background_single_signficant_pvalues/MB-E10-5_chr1_Eya1.png',
output_folder + '/MB-E10-5_chr1_Eya1.png', tolerance)
assert res is None, res
res = compare_images(
ROOT +
'chicPlotViewpoint/background_single_signficant_pvalues/FL-E13-5_chr1_Sox17.png',
output_folder + '/FL-E13-5_chr1_Sox17.png', tolerance)
assert res is None, res
res = compare_images(
ROOT +
'chicPlotViewpoint/background_single_signficant_pvalues/MB-E10-5_chr1_Sox17.png',
output_folder + '/MB-E10-5_chr1_Sox17.png', tolerance)
assert res is None, res
res = compare_images(
ROOT +
'chicPlotViewpoint/background_single_signficant_pvalues/FL-E13-5_chr1_Tfap2d.png',
output_folder + '/FL-E13-5_chr1_Tfap2d.png', tolerance)
assert res is None, res
res = compare_images(
ROOT +
'chicPlotViewpoint/background_single_signficant_pvalues/MB-E10-5_chr1_Tfap2d.png',
output_folder + '/MB-E10-5_chr1_Tfap2d.png', tolerance)
assert res is None, res
def test_one_viewpoint_colormap_pvalue_truncate_zeros():
outfile = NamedTemporaryFile(suffix='.png', delete=False)
outfile.close()
args = "-if {} --range {} {} --pValue --colorMapPvalue {} -o {} --pValue --colorMapPvalue plasma --maxPValue 0.5 --minPValue 0.1 -t {} --truncateZeroPvalues".format(
ROOT +
'chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt',
200000, 200000, 'plasma', outfile.name, 1).split()
chicPlotViewpoint.main(args)
res = compare_images(ROOT + 'chicPlotViewpoint/two_viewpoint_pvalue.png',
outfile.name, tolerance)
assert res is None, res
def test_two_viewpoint_fileformat_dpi():
outfile = NamedTemporaryFile(suffix='.pdf', delete=False)
outfile.close()
args = "-if {} {} --range {} {} -o {} --dpi {} --outputFormat {} -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',
200000, 200000, outfile.name, 100, 'pdf', 1).split()
chicPlotViewpoint.main(args)
res = compare_images(ROOT + 'chicPlotViewpoint/two_viewpoint.pdf',
outfile.name, tolerance)
assert res is None, res
def test_one_viewpoint():
outfile = NamedTemporaryFile(suffix='.png', delete=False)
outfile.close()
args = "-if {} --range {} {} -o {}".format(
ROOT +
'chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed',
200000, 200000, outfile.name).split()
chicPlotViewpoint.main(args)
res = compare_images(
ROOT +
'chicPlotViewpoint/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.png',
outfile.name, tolerance)
assert res is None, res
def test_two_viewpoint_background_differential():
outfile = NamedTemporaryFile(suffix='.png', delete=False)
outfile.close()
args = "-if {} {} --range {} {} -o {} -bmf {} --differentialTestResult {} -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',
200000, 200000, outfile.name, ROOT + 'background.txt', ROOT +
'chicDifferentialTest/batch_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt',
1).split()
chicPlotViewpoint.main(args)
res = compare_images(
ROOT + 'chicPlotViewpoint/two_viewpoint_background_differential.png',
outfile.name, tolerance)
assert res is None, res
def test_two_viewpoint_background_significant():
outfile = NamedTemporaryFile(suffix='.png', delete=False)
outfile.close()
args = "-if {} {} --range {} {} -o {} -bmf {} --significantInteractions {} {} -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',
200000, 200000, outfile.name, ROOT + 'background.txt', ROOT +
'chicSignificantInteractions/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt',
ROOT +
'chicSignificantInteractions/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt',
1).split()
chicPlotViewpoint.main(args)
res = compare_images(
ROOT + 'chicPlotViewpoint/two_viewpoint_background_significant.png',
outfile.name, tolerance)
assert res is None, res
def test_one_gene():
outfile = NamedTemporaryFile(suffix='.tar.gz', delete=False)
outfile.close()
args = "-if {} --range {} {} -o {} -t {} --combinationMode oneGene --combinationName Eya1".format(
ROOT + 'chicViewpoint/two_matrices.hdf5', 200000, 200000, outfile.name,
1).split()
chicPlotViewpoint.main(args)
file_obj = tarfile.open(outfile.name, "r")
namelist = file_obj.getnames()
assert len(namelist) == 3
assert 'FL-E13-5_chr1_Eya1.png' in namelist
output_folder = mkdtemp(prefix="output_")
file_obj.extractall(output_folder)
res = compare_images(
ROOT +
'chicPlotViewpoint/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.png',
output_folder + '/FL-E13-5_chr1_Eya1.png', tolerance)
assert res is None, res
