genipe.tests package

Module contents

Submodules

genipe.tests.test_db module

class genipe.tests.test_db.TestDB(methodName='runTest')

Bases: unittest.case.TestCase

setUp()

Setup the tests.

tearDown()

Finishes the test.

test_check_task_completion()

Tests the ‘check_task_completion’ function.

test_create_db_connection()

Tests the ‘_create_db_connection’ function.

test_create_task_db()

Tests the ‘create_task_db’ function.

test_create_task_entry()

Tests the ‘create_task_entry’ function.

test_get_all_runtimes()

Tests the ‘get_all_runtimes’ function.

test_get_task_runtime()

Tests the ‘task_runtime’ function.

test_mark_drmaa_task_completed()

Tests the ‘mark_drmaa_task_completed’ function.

test_mark_task_completed()

Tests the ‘mark_task_completed’ function.

test_mark_task_incomplete()

Tests the ‘mark_task_incomplete’ function.

genipe.tests.test_formats module

class genipe.tests.test_formats.TestFormats(methodName='runTest')

Bases: unittest.case.TestCase

test_additive_from_probs()

Tests the ‘additive_from_probs’ function.

test_dosage_from_probs()

Tests the ‘dosage_from_probs’ function.

test_get_good_probs()

Tests the ‘get_good_probs’ function.

test_hard_calls_from_probs()

Tests the ‘hard_calls_from_probs’ function.

test_maf_dosage_from_probs()

Tests the ‘maf_dosage_from_probs’ function.

test_maf_from_probs()

Tests the ‘maf_from_probs’ function.

test_matrix_from_line()

Tests the ‘matrix_from_line’ function.

genipe.tests.test_impute2_extractor module

class genipe.tests.test_impute2_extractor.TestImpute2Extractor(methodName='runTest')

Bases: unittest.case.TestCase

static clean_logging_handlers()

setUp()

Setup the tests.

tearDown()

Finishes the test.

test_extract()

Tests the extraction by marker name.

test_genomic()

Tests the extraction by genomic location.

test_genomic_info()

Tests the extraction by genomic location and information value.

test_genomic_maf()

Tests the extraction by genomic location and maf.

test_genomic_maf_info()

Tests the extraction by genomic location, maf and information.

test_genomic_maf_rate()

Tests the extraction by genomic location, maf and rate.

test_genomic_maf_rate_info()

Tests the extraction by genomic location, maf, rate and info.

test_genomic_rate()

Tests the extraction by genomic location and completion rate.

test_info()

Tests the extraction by information value.

test_maf()

Tests the extraction by maf.

test_maf_info()

Tests the extraction by maf and information value.

test_maf_rate()

Tests the extraction by maf and completion rate.

test_maf_rate_info()

Tests the extraction by maf, completion rate and information.

test_rate()

Tests the extraction by completion rate.

test_rate_info()

Tests the extraction by completion rate and information value.

genipe.tests.test_impute2_merger module

class genipe.tests.test_impute2_merger.TestImpute2Merger(methodName='runTest')

Bases: unittest.case.TestCase

static clean_logging_handlers()

setUp()

Setup the tests.

tearDown()

Finishes the test.

test_check_alleles()

Checks the ‘.alleles’ file.

test_check_output_files()

Checks the presence of all the output files.

test_completion_rates()

Checks the ‘.completion_rates’ file.

test_good_sites()

Checks the ‘.good_sites’ file.

test_impute2()

Checks the ‘.impute2’ file.

test_impute2_info()

Checks the ‘.impute2_info’ file.

test_imputed_sites()

Checks the ‘.imputed_sites’ file.

test_maf()

Checks the ‘.maf’ file.

test_map()

Checks the ‘.map’ file.

genipe.tests.test_imputed_stats module

class genipe.tests.test_imputed_stats.TestImputedStats(methodName='runTest')

Bases: unittest.case.TestCase

setUp()

Setup the tests.

tearDown()

Finishes the test.

test_check_args()

Tests the ‘check_args’ function.

test_compute_statistics()

Tests the ‘compute_statistics’ function.

test_get_formula()

Tests the ‘get_formula’ function.

test_process_impute2_site()

Tests the ‘process_impute2_site’ function.

test_read_phenotype()

Tests the ‘read_phenotype’ function.

test_read_samples()

Tests the ‘read_samples’ function.

test_read_sites_to_extract()

Tests the ‘test_read_sites_to_extract’ function.

test_samples_with_hetero_calls()

Tests the ‘samples_with_hetero_calls’ function.

class genipe.tests.test_imputed_stats.TestImputedStatsCox(methodName='runTest')

Bases: unittest.case.TestCase

setUp()

Setup the tests.

tearDown()

Finishes the test.

test_fit_cox_interaction_snp1()

Tests the ‘fit_cox’ function with interaction, first SNP.

test_fit_cox_invalid()

Tests the ‘fit_linear’ function, third SNP.

test_fit_cox_snp1()

Tests the ‘fit_cox’ function, first SNP.

test_fit_cox_snp2()

Tests the ‘fit_cox’ function, second SNP.

test_fit_cox_snp3()

Tests the ‘fit_cox’ function, third SNP.

test_full_fit_cox()

Tests the full pipeline for Cox’s regression.

test_full_fit_cox_interaction()

Tests the full pipeline for Cox’s regression with interaction.

test_full_fit_cox_multiprocess()

Tests the full pipeline for Cox’s regression with >1 processes.

class genipe.tests.test_imputed_stats.TestImputedStatsLinear(methodName='runTest')

Bases: unittest.case.TestCase

setUp()

Setup the tests.

tearDown()

Finishes the test.

test_fit_linear_interaction()

Tests the ‘fit_linear’ function with interaction.

test_fit_linear_invalid()

Tests the ‘fit_linear’ function, invalid values.

test_fit_linear_snp1()

Tests the ‘fit_linear’ function, first SNP.

test_fit_linear_snp2()

Tests the ‘fit_linear’ function, second SNP.

test_fit_linear_snp3()

Tests the ‘fit_linear’ function, third SNP.

test_full_fit_linear()

Tests the full pipeline for linear regression.

test_full_fit_linear_interaction()

Tests the full pipeline for linear regression with interaction.

test_full_fit_linear_multiprocess()

Tests the full pipeline for linear regression with >1 processes.

class genipe.tests.test_imputed_stats.TestImputedStatsLogistic(methodName='runTest')

Bases: unittest.case.TestCase

setUp()

Setup the tests.

tearDown()

Finishes the test.

test_fit_logistic_interaction()

Tests the ‘fit_logistic’ function with interaction.

test_fit_logistic_invalid()

Tests the ‘fit_logistic’ function, invalid values.

test_fit_logistic_snp1()

Tests the ‘fit_logistic’ function, first SNP.

test_fit_logistic_snp2()

Tests the ‘fit_logistic’ function, second SNP.

test_fit_logistic_snp3()

Tests the ‘fit_logistic’ function, third SNP.

test_full_fit_logistic()

Tests the full pipeline for logistic regression.

test_full_fit_logistic_interaction()

Tests the full pipeline for logistic regression with interaction.

test_full_fit_logistic_multiprocess()

Tests the full pipeline, logistic regression with >1 processes.

class genipe.tests.test_imputed_stats.TestImputedStatsMixedLM(methodName='runTest')

Bases: unittest.case.TestCase

setUp()

Setup the tests.

classmethod setUpClass()

Gets the data and compute random effects.

tearDown()

Finishes the test.

test_fit_mixedlm_interaction()

Tests the ‘fit_mixedlm’ function with interaction.

test_fit_mixedlm_interaction_use_ml()

Tests the ‘fit_mixedlm’ function with interaction (using ML).

test_fit_mixedlm_invalid_column()

Tests when asking an invalid column.

test_fit_mixedlm_snp1()

Tests the ‘fit_mixedlm’ function for the first SNP.

test_fit_mixedlm_snp1_use_ml()

Tests mixedlm using ML on first SNP.

test_fit_mixedlm_snp2()

Tests the ‘fit_mixedlm’ function for the second SNP.

test_fit_mixedlm_snp2_use_ml()

Tests mixedlm using ML on second SNP.

test_fit_mixedlm_snp3()

Tests the ‘fit_mixedlm’ function for the third SNP.

test_fit_mixedlm_snp3_use_ml()

Tests mixedlm using ML on third SNP.

test_full_fit_mixedlm()

Tests the full pipeline for mixed effect model.

test_full_fit_mixedlm_interaction()

Tests the full pipeline for mixed linear model with interaction.

test_full_fit_mixedlm_interaction_use_ml()

Tests the full pipeline for mixed linear model (interaction, ML).

test_full_fit_mixedlm_multiprocess()

Tests the full pipeline, mixed linear model with >1 processes.

test_full_fit_mixedlm_multiprocess_use_ml()

Tests the full pipeline, mixed linear with >1 processes (ML).

test_full_fit_mixedlm_use_ml()

Tests the full pipeline for mixed effect model (using ML).

class genipe.tests.test_imputed_stats.TestImputedStatsSkat(methodName='runTest')

Bases: unittest.case.TestCase

args = None

classmethod setUpClass()

Hook method for setting up class fixture before running tests in the class.

static setup_skat_files(out_directory)

Parses the SKAT example files into the format expected by genipe.

classmethod tearDownClass()

Hook method for deconstructing the class fixture after running all tests in the class.

test_continuous()

test_continuous_multiprocess()

test_discrete()

test_discrete_multiprocess()

tmp_dir = None

genipe.tests.test_launcher module

class genipe.tests.test_launcher.TestLauncher(methodName='runTest')

Bases: unittest.case.TestCase

setUp()

Setup the tests.

tearDown()

Finishes the test.

test_check_impute2_file()

Tests the ‘_check_impute2_file’ function.

test_check_missing_impute2()

Tests the ‘_check_output_files’ for missing impute2 file.

test_check_output_files()

Tests the ‘_check_output_files’ function.

genipe.tests.test_main_pipeline module

class genipe.tests.test_main_pipeline.TestMainPipeline(methodName='runTest')

Bases: unittest.case.TestCase

setUp()

Setup the tests.

tearDown()

Finishes the test.

test_file_sorter()

Tests the ‘file_sorter’ function.

test_gather_execution_time()

Tests the ‘gather_execution_time’ function.

test_gather_imputation_stats()

Tests the ‘gather_imputation_stats’ function.

test_gather_maf_stats()

Tests the ‘gather_maf_stats’ function.

test_get_chrom_encoding()

Tests the ‘get_chrom_encoding’ function.

test_get_chromosome_length()

Tests the ‘get_chromosome_length’ function.

test_get_cross_validation_results()

Tests the ‘get_cross_validation_results’ function.

test_is_reversed()

Tests the ‘is_reversed’ function.

test_read_preamble()

Tests the ‘read_preamble’ function.

genipe.tests.test_reporting_utils module

class genipe.tests.test_reporting_utils.TestReportingUtils(methodName='runTest')

Bases: unittest.case.TestCase

test_colorize_time()

Tests the ‘colorize_time’ function.

test_create_float()

Tests the ‘create_float’ function.

test_create_tabular()

Tests the ‘create_tabular’ function.

test_format_tex()

Tests the ‘format_tex’ function.

test_format_time()

Tests the ‘format_time’ function.

test_is_sanitized()

Tests the ‘_is_sanitized’ function.

test_sanitize_tex()

Tests the ‘sanitize_tex’ function.

test_tex_inline_math()

Tests the ‘tex_inline_math’ function.

test_wrap_tex()

Tests the ‘wrap_tex’ function.