Index

A

additive_from_probs() (in module genipe.formats.impute2)

args (genipe.tests.test_imputed_stats.TestImputedStatsSkat attribute)

C

check_args() (in module genipe.tools.impute2_extractor) (in module genipe.tools.impute2_merger) (in module genipe.tools.imputed_stats) check_files() (in module genipe.tools.genipe_tutorial) check_task_completion() (in module genipe.db.utils) clean_logging_handlers() (genipe.tests.test_impute2_extractor.TestImpute2Extractor static method) (genipe.tests.test_impute2_merger.TestImpute2Merger static method)

colorize_time() (in module genipe.reporting.utils) compute_statistics() (in module genipe.tools.imputed_stats) concatenate_files() (in module genipe.tools.impute2_merger) config_jinja2() (in module genipe.reporting.utils) create_float() (in module genipe.reporting.utils) create_tabular() (in module genipe.reporting.utils) create_task_db() (in module genipe.db.utils) create_task_entry() (in module genipe.db.utils)

D

dosage_from_probs() (in module genipe.formats.impute2)

download_file() (in module genipe.tools.genipe_tutorial)

E

extract_companion_files() (in module genipe.tools.impute2_extractor)

extract_markers() (in module genipe.tools.impute2_extractor)

F

fit_cox() (in module genipe.tools.imputed_stats) fit_linear() (in module genipe.tools.imputed_stats) fit_logistic() (in module genipe.tools.imputed_stats)

fit_mixedlm() (in module genipe.tools.imputed_stats) format_tex() (in module genipe.reporting.utils) format_time() (in module genipe.reporting.utils)

G

gather_extraction() (in module genipe.tools.impute2_extractor) generate_bash() (in module genipe.tools.genipe_tutorial) generate_report() (in module genipe.reporting.autoreport) genipe module genipe.config module genipe.config.parser module genipe.db module genipe.db.utils module genipe.error module genipe.formats module genipe.formats.impute2 module genipe.formats.index module genipe.pipeline module genipe.reporting module genipe.reporting.autoreport module genipe.reporting.utils module genipe.task module genipe.task.launcher module genipe.tests module genipe.tests.test_db module genipe.tests.test_formats module

genipe.tests.test_impute2_extractor module genipe.tests.test_impute2_merger module genipe.tests.test_imputed_stats module genipe.tests.test_launcher module genipe.tests.test_main_pipeline module genipe.tests.test_reporting_utils module genipe.tools module genipe.tools.genipe_tutorial module genipe.tools.impute2_extractor module genipe.tools.impute2_merger module genipe.tools.imputed_stats module genipe.version module GenipeError get_all_runtimes() (in module genipe.db.utils) get_file_prefix() (in module genipe.tools.impute2_extractor) get_formula() (in module genipe.tools.imputed_stats) get_genotypes() (in module genipe.tools.genipe_tutorial) get_good_probs() (in module genipe.formats.impute2) get_hg19() (in module genipe.tools.genipe_tutorial) get_impute2() (in module genipe.tools.genipe_tutorial) get_impute2_ref() (in module genipe.tools.genipe_tutorial) get_index() (in module genipe.formats.index) get_open_func() (in module genipe.formats.index) get_os_info() (in module genipe.tools.genipe_tutorial) get_plink() (in module genipe.tools.genipe_tutorial) get_samples() (in module genipe.tools.impute2_extractor) get_shapeit() (in module genipe.tools.genipe_tutorial) get_task_runtime() (in module genipe.db.utils)

H

hard_calls_from_probs() (in module genipe.formats.impute2)

I

index_file() (in module genipe.tools.impute2_extractor)

is_file_like() (in module genipe.tools.imputed_stats)

L

launch_tasks() (in module genipe.task.launcher)

M

maf_dosage_from_probs() (in module genipe.formats.impute2) maf_from_probs() (in module genipe.formats.impute2) main() (in module genipe.tools.genipe_tutorial) (in module genipe.tools.impute2_extractor) (in module genipe.tools.impute2_merger) (in module genipe.tools.imputed_stats) mark_drmaa_task_completed() (in module genipe.db.utils) mark_task_completed() (in module genipe.db.utils) mark_task_incomplete() (in module genipe.db.utils) matrix_from_line() (in module genipe.formats.impute2) module genipe genipe.config genipe.config.parser genipe.db genipe.db.utils genipe.error genipe.formats genipe.formats.impute2 genipe.formats.index genipe.pipeline genipe.reporting genipe.reporting.autoreport genipe.reporting.utils genipe.task genipe.task.launcher genipe.tests genipe.tests.test_db genipe.tests.test_formats genipe.tests.test_impute2_extractor genipe.tests.test_impute2_merger genipe.tests.test_imputed_stats genipe.tests.test_launcher genipe.tests.test_main_pipeline genipe.tests.test_reporting_utils genipe.tools genipe.tools.genipe_tutorial genipe.tools.impute2_extractor genipe.tools.impute2_merger genipe.tools.imputed_stats genipe.version

P

parse_args() (in module genipe.tools.genipe_tutorial) (in module genipe.tools.impute2_extractor) (in module genipe.tools.impute2_merger) (in module genipe.tools.imputed_stats)

parse_drmaa_config() (in module genipe.config.parser) print_data() (in module genipe.tools.impute2_extractor) process_impute2_site() (in module genipe.tools.imputed_stats)

R

read_phenotype() (in module genipe.tools.imputed_stats)

read_samples() (in module genipe.tools.imputed_stats) read_sites_to_extract() (in module genipe.tools.imputed_stats)

S

samples_with_hetero_calls() (in module genipe.tools.imputed_stats) sanitize_tex() (in module genipe.reporting.utils) setUp() (genipe.tests.test_db.TestDB method) (genipe.tests.test_impute2_extractor.TestImpute2Extractor method) (genipe.tests.test_impute2_merger.TestImpute2Merger method) (genipe.tests.test_imputed_stats.TestImputedStats method) (genipe.tests.test_imputed_stats.TestImputedStatsCox method) (genipe.tests.test_imputed_stats.TestImputedStatsLinear method) (genipe.tests.test_imputed_stats.TestImputedStatsLogistic method) (genipe.tests.test_imputed_stats.TestImputedStatsMixedLM method) (genipe.tests.test_launcher.TestLauncher method) (genipe.tests.test_main_pipeline.TestMainPipeline method)

setup_skat_files() (genipe.tests.test_imputed_stats.TestImputedStatsSkat static method) setUpClass() (genipe.tests.test_imputed_stats.TestImputedStatsMixedLM class method) (genipe.tests.test_imputed_stats.TestImputedStatsSkat class method) skat_parse_impute2() (in module genipe.tools.imputed_stats) skat_read_snp_set() (in module genipe.tools.imputed_stats)

T

tearDown() (genipe.tests.test_db.TestDB method) (genipe.tests.test_impute2_extractor.TestImpute2Extractor method) (genipe.tests.test_impute2_merger.TestImpute2Merger method) (genipe.tests.test_imputed_stats.TestImputedStats method) (genipe.tests.test_imputed_stats.TestImputedStatsCox method) (genipe.tests.test_imputed_stats.TestImputedStatsLinear method) (genipe.tests.test_imputed_stats.TestImputedStatsLogistic method) (genipe.tests.test_imputed_stats.TestImputedStatsMixedLM method) (genipe.tests.test_launcher.TestLauncher method) (genipe.tests.test_main_pipeline.TestMainPipeline method) tearDownClass() (genipe.tests.test_imputed_stats.TestImputedStatsSkat class method) test() (in module genipe) test_additive_from_probs() (genipe.tests.test_formats.TestFormats method) test_check_alleles() (genipe.tests.test_impute2_merger.TestImpute2Merger method) test_check_args() (genipe.tests.test_imputed_stats.TestImputedStats method) test_check_impute2_file() (genipe.tests.test_launcher.TestLauncher method) test_check_missing_impute2() (genipe.tests.test_launcher.TestLauncher method) test_check_output_files() (genipe.tests.test_impute2_merger.TestImpute2Merger method) (genipe.tests.test_launcher.TestLauncher method) test_check_task_completion() (genipe.tests.test_db.TestDB method) test_colorize_time() (genipe.tests.test_reporting_utils.TestReportingUtils method) test_completion_rates() (genipe.tests.test_impute2_merger.TestImpute2Merger method) test_compute_statistics() (genipe.tests.test_imputed_stats.TestImputedStats method) test_continuous() (genipe.tests.test_imputed_stats.TestImputedStatsSkat method) test_continuous_multiprocess() (genipe.tests.test_imputed_stats.TestImputedStatsSkat method) test_create_db_connection() (genipe.tests.test_db.TestDB method) test_create_float() (genipe.tests.test_reporting_utils.TestReportingUtils method) test_create_tabular() (genipe.tests.test_reporting_utils.TestReportingUtils method) test_create_task_db() (genipe.tests.test_db.TestDB method) test_create_task_entry() (genipe.tests.test_db.TestDB method) test_discrete() (genipe.tests.test_imputed_stats.TestImputedStatsSkat method) test_discrete_multiprocess() (genipe.tests.test_imputed_stats.TestImputedStatsSkat method) test_dosage_from_probs() (genipe.tests.test_formats.TestFormats method) test_extract() (genipe.tests.test_impute2_extractor.TestImpute2Extractor method) test_file_sorter() (genipe.tests.test_main_pipeline.TestMainPipeline method) test_fit_cox_interaction_snp1() (genipe.tests.test_imputed_stats.TestImputedStatsCox method) test_fit_cox_invalid() (genipe.tests.test_imputed_stats.TestImputedStatsCox method) test_fit_cox_snp1() (genipe.tests.test_imputed_stats.TestImputedStatsCox method) test_fit_cox_snp2() (genipe.tests.test_imputed_stats.TestImputedStatsCox method) test_fit_cox_snp3() (genipe.tests.test_imputed_stats.TestImputedStatsCox method) test_fit_linear_interaction() (genipe.tests.test_imputed_stats.TestImputedStatsLinear method) test_fit_linear_invalid() (genipe.tests.test_imputed_stats.TestImputedStatsLinear method) test_fit_linear_snp1() (genipe.tests.test_imputed_stats.TestImputedStatsLinear method) test_fit_linear_snp2() (genipe.tests.test_imputed_stats.TestImputedStatsLinear method) test_fit_linear_snp3() (genipe.tests.test_imputed_stats.TestImputedStatsLinear method) test_fit_logistic_interaction() (genipe.tests.test_imputed_stats.TestImputedStatsLogistic method) test_fit_logistic_invalid() (genipe.tests.test_imputed_stats.TestImputedStatsLogistic method) test_fit_logistic_snp1() (genipe.tests.test_imputed_stats.TestImputedStatsLogistic method) test_fit_logistic_snp2() (genipe.tests.test_imputed_stats.TestImputedStatsLogistic method) test_fit_logistic_snp3() (genipe.tests.test_imputed_stats.TestImputedStatsLogistic method) test_fit_mixedlm_interaction() (genipe.tests.test_imputed_stats.TestImputedStatsMixedLM method) test_fit_mixedlm_interaction_use_ml() (genipe.tests.test_imputed_stats.TestImputedStatsMixedLM method) test_fit_mixedlm_invalid_column() (genipe.tests.test_imputed_stats.TestImputedStatsMixedLM method) test_fit_mixedlm_snp1() (genipe.tests.test_imputed_stats.TestImputedStatsMixedLM method) test_fit_mixedlm_snp1_use_ml() (genipe.tests.test_imputed_stats.TestImputedStatsMixedLM method) test_fit_mixedlm_snp2() (genipe.tests.test_imputed_stats.TestImputedStatsMixedLM method) test_fit_mixedlm_snp2_use_ml() (genipe.tests.test_imputed_stats.TestImputedStatsMixedLM method) test_fit_mixedlm_snp3() (genipe.tests.test_imputed_stats.TestImputedStatsMixedLM method) test_fit_mixedlm_snp3_use_ml() (genipe.tests.test_imputed_stats.TestImputedStatsMixedLM method) test_format_tex() (genipe.tests.test_reporting_utils.TestReportingUtils method) test_format_time() (genipe.tests.test_reporting_utils.TestReportingUtils method) test_full_fit_cox() (genipe.tests.test_imputed_stats.TestImputedStatsCox method) test_full_fit_cox_interaction() (genipe.tests.test_imputed_stats.TestImputedStatsCox method) test_full_fit_cox_multiprocess() (genipe.tests.test_imputed_stats.TestImputedStatsCox method) test_full_fit_linear() (genipe.tests.test_imputed_stats.TestImputedStatsLinear method) test_full_fit_linear_interaction() (genipe.tests.test_imputed_stats.TestImputedStatsLinear method) test_full_fit_linear_multiprocess() (genipe.tests.test_imputed_stats.TestImputedStatsLinear method) test_full_fit_logistic() (genipe.tests.test_imputed_stats.TestImputedStatsLogistic method) test_full_fit_logistic_interaction() (genipe.tests.test_imputed_stats.TestImputedStatsLogistic method)

test_full_fit_logistic_multiprocess() (genipe.tests.test_imputed_stats.TestImputedStatsLogistic method) test_full_fit_mixedlm() (genipe.tests.test_imputed_stats.TestImputedStatsMixedLM method) test_full_fit_mixedlm_interaction() (genipe.tests.test_imputed_stats.TestImputedStatsMixedLM method) test_full_fit_mixedlm_interaction_use_ml() (genipe.tests.test_imputed_stats.TestImputedStatsMixedLM method) test_full_fit_mixedlm_multiprocess() (genipe.tests.test_imputed_stats.TestImputedStatsMixedLM method) test_full_fit_mixedlm_multiprocess_use_ml() (genipe.tests.test_imputed_stats.TestImputedStatsMixedLM method) test_full_fit_mixedlm_use_ml() (genipe.tests.test_imputed_stats.TestImputedStatsMixedLM method) test_gather_execution_time() (genipe.tests.test_main_pipeline.TestMainPipeline method) test_gather_imputation_stats() (genipe.tests.test_main_pipeline.TestMainPipeline method) test_gather_maf_stats() (genipe.tests.test_main_pipeline.TestMainPipeline method) test_genomic() (genipe.tests.test_impute2_extractor.TestImpute2Extractor method) test_genomic_info() (genipe.tests.test_impute2_extractor.TestImpute2Extractor method) test_genomic_maf() (genipe.tests.test_impute2_extractor.TestImpute2Extractor method) test_genomic_maf_info() (genipe.tests.test_impute2_extractor.TestImpute2Extractor method) test_genomic_maf_rate() (genipe.tests.test_impute2_extractor.TestImpute2Extractor method) test_genomic_maf_rate_info() (genipe.tests.test_impute2_extractor.TestImpute2Extractor method) test_genomic_rate() (genipe.tests.test_impute2_extractor.TestImpute2Extractor method) test_get_all_runtimes() (genipe.tests.test_db.TestDB method) test_get_chrom_encoding() (genipe.tests.test_main_pipeline.TestMainPipeline method) test_get_chromosome_length() (genipe.tests.test_main_pipeline.TestMainPipeline method) test_get_cross_validation_results() (genipe.tests.test_main_pipeline.TestMainPipeline method) test_get_formula() (genipe.tests.test_imputed_stats.TestImputedStats method) test_get_good_probs() (genipe.tests.test_formats.TestFormats method) test_get_task_runtime() (genipe.tests.test_db.TestDB method) test_good_sites() (genipe.tests.test_impute2_merger.TestImpute2Merger method) test_hard_calls_from_probs() (genipe.tests.test_formats.TestFormats method) test_impute2() (genipe.tests.test_impute2_merger.TestImpute2Merger method) test_impute2_info() (genipe.tests.test_impute2_merger.TestImpute2Merger method) test_imputed_sites() (genipe.tests.test_impute2_merger.TestImpute2Merger method) test_info() (genipe.tests.test_impute2_extractor.TestImpute2Extractor method) test_is_reversed() (genipe.tests.test_main_pipeline.TestMainPipeline method) test_is_sanitized() (genipe.tests.test_reporting_utils.TestReportingUtils method) test_maf() (genipe.tests.test_impute2_extractor.TestImpute2Extractor method) (genipe.tests.test_impute2_merger.TestImpute2Merger method) test_maf_dosage_from_probs() (genipe.tests.test_formats.TestFormats method) test_maf_from_probs() (genipe.tests.test_formats.TestFormats method) test_maf_info() (genipe.tests.test_impute2_extractor.TestImpute2Extractor method) test_maf_rate() (genipe.tests.test_impute2_extractor.TestImpute2Extractor method) test_maf_rate_info() (genipe.tests.test_impute2_extractor.TestImpute2Extractor method) test_map() (genipe.tests.test_impute2_merger.TestImpute2Merger method) test_mark_drmaa_task_completed() (genipe.tests.test_db.TestDB method) test_mark_task_completed() (genipe.tests.test_db.TestDB method) test_mark_task_incomplete() (genipe.tests.test_db.TestDB method) test_matrix_from_line() (genipe.tests.test_formats.TestFormats method) test_process_impute2_site() (genipe.tests.test_imputed_stats.TestImputedStats method) test_rate() (genipe.tests.test_impute2_extractor.TestImpute2Extractor method) test_rate_info() (genipe.tests.test_impute2_extractor.TestImpute2Extractor method) test_read_phenotype() (genipe.tests.test_imputed_stats.TestImputedStats method) test_read_preamble() (genipe.tests.test_main_pipeline.TestMainPipeline method) test_read_samples() (genipe.tests.test_imputed_stats.TestImputedStats method) test_read_sites_to_extract() (genipe.tests.test_imputed_stats.TestImputedStats method) test_samples_with_hetero_calls() (genipe.tests.test_imputed_stats.TestImputedStats method) test_sanitize_tex() (genipe.tests.test_reporting_utils.TestReportingUtils method) test_tex_inline_math() (genipe.tests.test_reporting_utils.TestReportingUtils method) test_wrap_tex() (genipe.tests.test_reporting_utils.TestReportingUtils method) TestDB (class in genipe.tests.test_db) TestFormats (class in genipe.tests.test_formats) TestImpute2Extractor (class in genipe.tests.test_impute2_extractor) TestImpute2Merger (class in genipe.tests.test_impute2_merger) TestImputedStats (class in genipe.tests.test_imputed_stats) TestImputedStatsCox (class in genipe.tests.test_imputed_stats) TestImputedStatsLinear (class in genipe.tests.test_imputed_stats) TestImputedStatsLogistic (class in genipe.tests.test_imputed_stats) TestImputedStatsMixedLM (class in genipe.tests.test_imputed_stats) TestImputedStatsSkat (class in genipe.tests.test_imputed_stats) TestLauncher (class in genipe.tests.test_launcher) TestMainPipeline (class in genipe.tests.test_main_pipeline) TestReportingUtils (class in genipe.tests.test_reporting_utils) tex_inline_math() (in module genipe.reporting.utils) tmp_dir (genipe.tests.test_imputed_stats.TestImputedStatsSkat attribute)

U

untar_file() (in module genipe.tools.genipe_tutorial)

W

wrap_tex() (in module genipe.reporting.utils)