genetest.tests package

Submodules

genetest.tests.test_configuration module

class genetest.tests.test_configuration.TestAnalysisConfiguration(methodName='runTest')

Bases: unittest.case.TestCase

Create an instance of the class that will use the named test method when executed. Raises a ValueError if the instance does not have a method with the specified name.

classmethod setUpClass()

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

classmethod tearDownClass()

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

test_extra_section()

Tests when there is an extra section.

test_invalid_genotype_format()

Tests when an invalid format for genotypes is asked.

test_invalid_phenotype_format()

Tests when an invalid format for phenotypes is asked.

test_invalid_test()

Tests when an invalid model for statistics is asked.

test_missing_genotype_format()

Tests when the genotype format is missing.

test_missing_phenotype_format()

Tests when the phenotype format is missing.

test_missing_section()

Tests when there is a missing section.

test_missing_test()

Tests when the statistics test is missing.

test_normal_functionality()

Tests the normal functionality.

genetest.tests.test_coxph module

class genetest.tests.test_coxph.TestStatsCoxPH(methodName='runTest')

Bases: unittest.case.TestCase

Tests the ‘StatsCoxPH’ class.

Create an instance of the class that will use the named test method when executed. Raises a ValueError if the instance does not have a method with the specified name.

setUp()

Hook method for setting up the test fixture before exercising it.

classmethod setUpClass()

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

classmethod tearDownClass()

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

test_coxph_gwas()

Tests coxph regression for GWAS.

test_coxph_gwas_inter()

Tests coxph regression for GWAS inter (failure: singular matrix).

test_coxph_snp1()

Tests coxph regression with the first SNP.

test_coxph_snp1_inter()

Tests coxph regression with the first SNP (interaction).

test_coxph_snp1_inter_categorical()

Tests coxph first SNP (interaction, category).

test_coxph_snp2()

Tests coxph regression with the second SNP.

test_coxph_snp2_inter()

Tests coxph regression with the second SNP (interaction).

test_coxph_snp3()

Tests coxph regression with the third SNP.

test_coxph_snp3_inter()

Tests coxph regression with the third SNP (interaction).

test_coxph_snp4()

Tests coxph regression with the third SNP.

test_coxph_snp4_inter()

Tests coxph regression with the third SNP (interaction).

genetest.tests.test_descriptive_stats module

class genetest.tests.test_descriptive_stats.TestDescriptiveStats(methodName='runTest')

Bases: unittest.case.TestCase

Tests the descriptive statistics module.

Create an instance of the class that will use the named test method when executed. Raises a ValueError if the instance does not have a method with the specified name.

test_get_maf_flip()

Tests when flip is required.

test_get_maf_flip_sex()

Tests when flip is required (sex).

test_get_maf_no_valid_genotypes()

Tests when all genotypes are missing.

test_get_maf_no_valid_genotypes_sex()

Tests when all genotypes are missing (sex).

test_get_maf_with_null()

Tests when there are missing genotypes.

test_get_maf_with_null_sex()

Tests when there are missing genotypes (sex).

test_get_maf_without_null()

Tests when there are no missing genotypes.

test_get_maf_without_null_sexes()

Tests when there are no missing genotypes (sex).

genetest.tests.test_linear module

class genetest.tests.test_linear.TestStatsLinear(methodName='runTest')

Bases: unittest.case.TestCase

Tests the ‘StatsLinear’ class.

Create an instance of the class that will use the named test method when executed. Raises a ValueError if the instance does not have a method with the specified name.

setUp()

Hook method for setting up the test fixture before exercising it.

classmethod setUpClass()

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

classmethod tearDownClass()

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

test_linear_gwas()

Tests linear regression for GWAS.

test_linear_gwas_inter()

Tests linear regression for GWAS with interaction.

test_linear_snp1()

Tests linear regression with the first SNP.

test_linear_snp1_inter()

Tests linear regression with the first SNP (interaction).

test_linear_snp1_inter_categorical()

Tests linear regression for first SNP (inter, category).

test_linear_snp2()

Tests linear regression with the second SNP.

test_linear_snp2_inter()

Tests linear regression with the second SNP (interaction).

test_linear_snp3()

Tests linear regression with the third SNP.

test_linear_snp3_inter()

Tests linear regression with the third SNP.

test_linear_snp4()

Tests linear regression with the fourth SNP.

test_linear_snp4_inter()

Tests linear regression with the fourth SNP (interaction).

test_linear_snp5()

Tests linear regression with the fifth SNP (raises StatsError).

test_linear_snp5_inter()

Tests linear regression fifth SNP (inter) (raises StatsError).

genetest.tests.test_logistic module

class genetest.tests.test_logistic.TestStatsLogistic(methodName='runTest')

Bases: unittest.case.TestCase

Tests the ‘StatsLogistic’ class.

Create an instance of the class that will use the named test method when executed. Raises a ValueError if the instance does not have a method with the specified name.

setUp()

Hook method for setting up the test fixture before exercising it.

classmethod setUpClass()

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

classmethod tearDownClass()

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

test_logistic_gwas()

Tests logistic regression for GWAS.

test_logistic_gwas_inter()

Tests logistic regression for GWAS with interaction.

test_logistic_snp1()

Tests logistic regression with the first SNP.

test_logistic_snp1_inter()

Tests logistic regression with the first SNP (interaction).

test_logistic_snp1_inter_categorical()

Tests logistic regression first SNP (inter, category).

test_logistic_snp2()

Tests logistic regression with the second SNP.

test_logistic_snp2_inter()

Tests logistic regression with the second SNP (interaction).

test_logistic_snp3()

Tests logistic regression with the third SNP (raises StatsError).

test_logistic_snp3_inter()

Tests logistic regression third SNP (raises StatsError, inter).

genetest.tests.test_mixedlm module

class genetest.tests.test_mixedlm.TestStatsMixedLM(methodName='runTest')

Bases: unittest.case.TestCase

Tests the ‘StatsMixedLM’ class.

Create an instance of the class that will use the named test method when executed. Raises a ValueError if the instance does not have a method with the specified name.

setUp()

Hook method for setting up the test fixture before exercising it.

classmethod setUpClass()

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

classmethod tearDownClass()

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

test_mixedlm_gwas()

Tests mixedlm regression for GWAS.

test_mixedlm_gwas_inter()

Tests mixedlm regression for GWAS with interaction.

test_mixedlm_snp1_inter_ml()

Tests mixedlm regression with the first SNP (using ML, inter).

test_mixedlm_snp1_inter_reml()

Tests mixedlm regression with the first SNP (using REML, inter).

test_mixedlm_snp1_ml()

Tests mixedlm regression with the first SNP (using ML).

test_mixedlm_snp1_reml()

Tests mixedlm regression with the first SNP (using REML).

test_mixedlm_snp2_inter_ml()

Tests mixedlm regression with the second SNP (using ML, inter).

test_mixedlm_snp2_inter_reml()

Tests mixedlm regression with the second SNP (using REML, inter).

test_mixedlm_snp2_ml()

Tests mixedlm regression with the second SNP (using ML).

test_mixedlm_snp2_reml()

Tests mixedlm regression with the second SNP (using REML).

test_mixedlm_snp3_inter_ml()

Tests mixedlm regression with the third SNP (using ML, inter).

test_mixedlm_snp3_inter_reml()

Tests mixedlm regression with the third SNP (using REML, inter).

test_mixedlm_snp3_ml()

Tests mixedlm regression with the third SNP (using ML).

test_mixedlm_snp3_reml()

Tests mixedlm regression with the third SNP (using REML).

test_mixedlm_snp4_inter_ml()

Tests mixedlm regression with the fourth SNP (using ML, inter).

test_mixedlm_snp4_inter_reml()

Tests mixedlm regression with the fourth SNP (using REML, inter).

test_mixedlm_snp4_ml()

Tests mixedlm regression with the fourth SNP (using ML).

test_mixedlm_snp4_reml()

Tests mixedlm regression with the fourth SNP (using REML).

genetest.tests.test_phenotypes module

class genetest.tests.test_phenotypes.TestCore(methodName='runTest')

Bases: unittest.case.TestCase

Create an instance of the class that will use the named test method when executed. Raises a ValueError if the instance does not have a method with the specified name.

test_close()

Tests that ‘close’ raises a NotImplementedError.

test_get_phenotypes()

Tests that ‘get_phenotypes’ raises a NotImplementedError.

test_get_sex_no_attribute()

Tests when the ‘_sex_column’ attribute is missing.

class genetest.tests.test_phenotypes.TestText(methodName='runTest')

Bases: unittest.case.TestCase

Create an instance of the class that will use the named test method when executed. Raises a ValueError if the instance does not have a method with the specified name.

setUp()

Hook method for setting up the test fixture before exercising it.

tearDown()

Hook method for deconstructing the test fixture after testing it.

test_bad_subset_phenotypes()

Tests asking for a subset with unavailable phenotypes.

test_duplicated_sex()

Tests when there are repeated (different) sex for a sample.

test_get_sex()

Tests asking for the sex series.

test_invalid_sex()

Tests when other values than 0, 1 and NaN are in the sex column.

test_multiple_missing_values()

Tests when there are multiple missing values.

test_normal_functionality()

Tests normal functionality.

test_one_other_missing_value()

Tests when there are other missing values.

test_repeated_measurements()

Tests when there are repeated measurements available.

test_specific_column_missing_value()

Tests when there are specific missing values for some columns.

test_string_representation()

Checks the string representation.

test_subset_phenotypes()

Tests asking for a subset of phenotypes.

test_undefined_sex_column()

Tests when the sex column wasn’t specified.

genetest.tests.test_stats_core module

class genetest.tests.test_stats_core.TestStatsLinear(methodName='runTest')

Bases: unittest.case.TestCase

Tests the ‘StatsLinear’ class.

Create an instance of the class that will use the named test method when executed. Raises a ValueError if the instance does not have a method with the specified name.

setUp()

Hook method for setting up the test fixture before exercising it.

test__create_model()

Tests the ‘_create_model’ function.

test__create_model_no_intercept()

Tests the ‘_create_model’ function with no intercept.

test__create_model_with_interaction()

Tests the ‘_create_model’ function with an interaction.

test__create_model_with_interaction2()

Tests with an interaction (categorical).

test__create_model_with_interaction_not_in_predictors()

Tests with an interaction but not in predictors list.

Module contents