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