Index

_

__post_init__() (aigct.repository.TableDef method) __tablename__ (aigct.db_model.VariantEffectGeneAuc attribute) (aigct.db_model.VariantEffectSource attribute) (aigct.db_model.VariantEffectTaskAuc attribute) _add_info_to_metric_dataframes() (aigct.analyzer.VEAnalyzer method) _analyzer (aigct.container.VEBenchmarkContainer attribute) _build_excep_where_clause() (aigct.etl.repo_loader.RepositoryLoader method) _cache (aigct.repository.VariantEffectLabelRepository attribute) (aigct.repository.VariantEffectScoreRepository attribute) (aigct.repository.VariantEffectSourceRepository attribute) (aigct.repository.VariantFilterRepository attribute) (aigct.repository.VariantRepository attribute) (aigct.repository.VariantTaskRepository attribute) _calibration_line_config (aigct.plotter.VEAnalysisPlotter attribute) _compute_general_metrics() (aigct.analyzer.VEAnalyzer static method) _compute_metrics() (aigct.analyzer.VEAnalyzer method) _compute_metrics_vs_threshold() (aigct.analyzer.VEAnalyzer method) _compute_mwu() (aigct.analyzer.VEAnalyzer method) _compute_num_unique_variants() (aigct.analyzer.VEAnalyzer static method) _compute_pr() (aigct.analyzer.VEAnalyzer method) _compute_pr_calibration_curves() (aigct.analyzer.VEAnalyzer method) _compute_roc() (aigct.analyzer.VEAnalyzer method) _compute_variant_counts() (aigct.query.VEBenchmarkQueryMgr static method) _config (aigct.plotter.VEAnalysisPlotter attribute) _convert_dot_to_nan() (aigct.etl.repo_loader.RepositoryLoader method) _data_folder_root (aigct.repository.RepoSessionContext attribute) _data_validator (aigct.container.VEBenchmarkContainer attribute) _derive_variant_effect_source_columns() (aigct.etl.repo_loader.RepositoryLoader method) _display_gene_metric_table() (aigct.plotter.VEAnalysisPlotter method) _display_mwu_table() (aigct.plotter.VEAnalysisPlotter method) _display_pr_table() (aigct.plotter.VEAnalysisPlotter method) _display_roc_table() (aigct.plotter.VEAnalysisPlotter method) _excep_file_full_path_name() (aigct.etl.repo_loader.RepositoryLoader method) _exporter (aigct.container.VEBenchmarkContainer attribute) _filter_repo (aigct.repository.VariantEffectLabelRepository attribute) (aigct.repository.VariantEffectScoreRepository attribute) _filter_scores_and_labels_by_genes() (aigct.analyzer.VEAnalyzer method) _get_gene_unique_variant_counts() (aigct.analyzer.VEAnalyzer method) _group_scores_into_bins() (aigct.analyzer.VEAnalyzer method) _init_once() (aigct.repository.DataCache method) (aigct.repository.TaskBasedDataCache method) (aigct.repository.TaskDataCache method) (aigct.repository.VariantCache method) (aigct.repository.VariantEffectLabelCache method) (aigct.repository.VariantEffectScoreCache method) (aigct.repository.VariantEffectSourceCache method) (aigct.repository.VariantFilterCache method) (aigct.repository.VariantTaskCache method) _instance (aigct.util.ParameterizedSingleton attribute) _label_repo (aigct.container.VEBenchmarkContainer attribute) _loader (aigct.etl.container.VEETLContainer attribute)

_lock (aigct.util.ParameterizedSingleton attribute) _log_folder (aigct.etl.repo_loader.RepositoryLoader attribute) _mwu_config (aigct.plotter.VEAnalysisPlotter attribute) _plot_binned_data() (aigct.plotter.VEAnalysisPlotter method) _plot_metrics_vs_threshold() (aigct.plotter.VEAnalysisPlotter method) _plot_mwu_bar() (aigct.plotter.VEAnalysisPlotter method) _plot_pr_curves() (aigct.plotter.VEAnalysisPlotter method) _plot_precision_recall_vs_threshold() (aigct.plotter.VEAnalysisPlotter method) _plot_precision_recall_vs_thresholds1() (aigct.plotter.VEAnalysisPlotter method) _plot_roc_curves() (aigct.plotter.VEAnalysisPlotter method) _plot_score_vs_pathogenic_fraction() (aigct.plotter.VEAnalysisPlotter method) _plot_score_vs_variant_counts() (aigct.plotter.VEAnalysisPlotter method) _plotter (aigct.container.VEBenchmarkContainer attribute) _query_mgr (aigct.container.VEBenchmarkContainer attribute) _remove_vep_genes_with_invalid_label_counts() (aigct.analyzer.VEAnalyzer method) _repo_context (aigct.etl.repo_loader.RepositoryLoader attribute) _repo_session_context (aigct.container.VEBenchmarkContainer attribute) (aigct.etl.container.VEETLContainer attribute) _reporter (aigct.container.VEBenchmarkContainer attribute) _roc_pr_config (aigct.plotter.VEAnalysisPlotter attribute) _score_repo (aigct.container.VEBenchmarkContainer attribute) _table_defs (aigct.repository.RepoSessionContext attribute) _task_full_path_name() (aigct.etl.repo_loader.RepositoryLoader method) _task_repo (aigct.repository.VariantEffectLabelRepository attribute) (aigct.repository.VariantEffectScoreRepository attribute) _upsert_repository_file() (aigct.etl.repo_loader.RepositoryLoader method) _validate_pk() (aigct.repo_qc.VEDataValidator method) _variant_effect_label_repo (aigct.analyzer.VEAnalyzer attribute) (aigct.query.VEBenchmarkQueryMgr attribute) (aigct.repo_qc.VEDataValidator attribute) _variant_effect_score_repo (aigct.analyzer.VEAnalyzer attribute) (aigct.query.VEBenchmarkQueryMgr attribute) (aigct.repo_qc.VEDataValidator attribute) (aigct.repository.VariantEffectSourceRepository attribute) _variant_effect_source_repo (aigct.analyzer.VEAnalyzer attribute) (aigct.container.VEBenchmarkContainer attribute) (aigct.query.VEBenchmarkQueryMgr attribute) (aigct.repo_qc.VEDataValidator attribute) _variant_filter_repo (aigct.container.VEBenchmarkContainer attribute) (aigct.query.VEBenchmarkQueryMgr attribute) (aigct.repo_qc.VEDataValidator attribute) _variant_repo (aigct.container.VEBenchmarkContainer attribute) (aigct.query.VEBenchmarkQueryMgr attribute) (aigct.repo_qc.VEDataValidator attribute) (aigct.repository.VariantEffectLabelRepository attribute) (aigct.repository.VariantEffectScoreRepository attribute) _variant_task_repo (aigct.container.VEBenchmarkContainer attribute) (aigct.query.VEBenchmarkQueryMgr attribute) (aigct.repo_qc.VEDataValidator attribute) _write_calibration_summary() (aigct.reporter.VEAnalysisReporter method) _write_metric_dataframe() (aigct.reporter.VEAnalysisReporter method) _write_summary() (aigct.reporter.VEAnalysisReporter method)

A

aigct module aigct.analyzer module aigct.check_install module aigct.config module aigct.container module aigct.context module aigct.date_util module aigct.db_model module aigct.etl module aigct.etl.container module aigct.etl.repo_loader module aigct.exporter module aigct.file_util module aigct.init_app module aigct.install_db module

aigct.install_util module aigct.model module aigct.pd_util module aigct.plot_util module aigct.plotter module aigct.query module aigct.query_util module aigct.repo_qc module aigct.report_util module aigct.reporter module aigct.repository module aigct.util module allele_frequency (aigct.model.VEQueryCriteria attribute) allele_frequency_operator (aigct.model.VEQueryCriteria attribute) alternate_nucleotide (aigct.model.VariantId attribute) analyzer (aigct.container.VEBenchmarkContainer property) auc (aigct.db_model.VariantEffectGeneAuc attribute) (aigct.db_model.VariantEffectTaskAuc attribute)

B

barchart() (in module aigct.plot_util)

Base (class in aigct.db_model) build_dataframe_where_clause() (in module aigct.pd_util)

C

check_install() (in module aigct.install_util) chromosome (aigct.model.VariantId attribute) cleanup_variant_query_params() (in module aigct.query) code (aigct.db_model.VariantEffectSource attribute) (aigct.model.VariantEffectSource attribute) column_name_map (aigct.model.VEQueryCriteria attribute)

COLUMN_NAME_MAP (in module aigct.etl.repo_loader) columns (aigct.repository.TableDef attribute) compute_calibration_metrics() (aigct.analyzer.VEAnalyzer method) compute_metrics() (aigct.analyzer.VEAnalyzer method) Config (class in aigct.util) create_feature_palette() (in module aigct.plot_util) create_folder() (in module aigct.file_util)

D

DATA_FOLDER (in module aigct.repository) data_folder_root (aigct.repository.RepoSessionContext property) data_frame (aigct.repository.DataCache property) data_validator (aigct.container.VEBenchmarkContainer property)

DataCache (class in aigct.repository) description (aigct.db_model.VariantEffectSource attribute) (aigct.model.VariantEffectSource attribute) dups_found (aigct.model.PkViolations attribute) (aigct.model.TaskPkViolations attribute)

E

export_calibration_results() (aigct.exporter.VEAnalysisExporter method)

export_results() (aigct.exporter.VEAnalysisExporter method) exporter (aigct.container.VEBenchmarkContainer property)

F

f1_curve_coordinates_df (aigct.model.VEAnalysisCalibrationResult attribute) file_name (aigct.repository.TableDef attribute) filter (aigct.model.VariantFilter attribute) filter_dataframe_by_list() (in module aigct.pd_util)

filter_genes (aigct.model.VariantFilter attribute) filter_names (aigct.model.VEQueryCriteria attribute) filter_variants (aigct.model.VariantFilter attribute) folder (aigct.repository.TableDef attribute) full_file_name (aigct.repository.TableDef attribute)

G

gene_aucs (aigct.db_model.VariantEffectSource attribute) gene_general_metrics (aigct.model.VEAnalysisResult attribute) gene_mwu_metrics (aigct.model.VEAnalysisResult attribute) gene_pr_curve_coordinates (aigct.model.VEAnalysisResult attribute) gene_pr_metrics (aigct.model.VEAnalysisResult attribute) gene_roc_curve_coordinates (aigct.model.VEAnalysisResult attribute) gene_roc_metrics (aigct.model.VEAnalysisResult attribute) gene_symbol (aigct.db_model.VariantEffectGeneAuc attribute) gene_symbols (aigct.model.VEQueryCriteria attribute) gene_unique_variant_counts_df (aigct.model.VEAnalysisResult attribute) GeneMetricSorter (class in aigct.report_util) general_metrics (aigct.model.VEAnalysisResult attribute) genome_assembly (aigct.model.VariantId attribute) get() (aigct.repository.VariantEffectLabelRepository method) (aigct.repository.VariantEffectScoreRepository method) (aigct.repository.VariantRepository method) get_all() (aigct.repository.VariantEffectSourceRepository method) (aigct.repository.VariantRepository method) (aigct.repository.VariantTaskRepository method) get_all_by_task() (aigct.repository.VariantEffectLabelRepository method) (aigct.repository.VariantEffectScoreRepository method) get_all_by_task_slim() (aigct.repository.VariantEffectScoreRepository method) get_all_for_all_tasks() (aigct.repository.VariantEffectLabelRepository method) (aigct.repository.VariantEffectScoreRepository method)

get_all_task_variant_effect_label_stats() (aigct.query.VEBenchmarkQueryMgr method) get_all_variant_effect_source_stats() (aigct.query.VEBenchmarkQueryMgr method) get_all_variant_filters() (aigct.query.VEBenchmarkQueryMgr method) get_all_variants() (aigct.query.VEBenchmarkQueryMgr method) get_analysis_scores_and_labels() (aigct.analyzer.VEAnalyzer method) get_by_code() (aigct.repository.VariantEffectSourceRepository method) get_by_task() (aigct.repository.VariantEffectSourceRepository method) (aigct.repository.VariantFilterRepository method) get_by_task_filter_name() (aigct.repository.VariantFilterRepository method) get_by_task_filter_names() (aigct.repository.VariantFilterRepository method) get_colors() (in module aigct.plot_util) get_data_frame() (aigct.repository.TaskBasedDataCache method) (aigct.repository.VariantEffectLabelCache method) get_data_frames() (aigct.repository.VariantFilterCache method) get_sample_config() (in module aigct.install_util) get_tasks() (aigct.query.VEBenchmarkQueryMgr method) get_variant_distribution() (aigct.query.VEBenchmarkQueryMgr method) get_variant_effect_scores() (aigct.query.VEBenchmarkQueryMgr method) get_variant_effect_source_stats() (aigct.query.VEBenchmarkQueryMgr method) get_variant_effect_sources() (aigct.query.VEBenchmarkQueryMgr method) get_variant_filter() (aigct.query.VEBenchmarkQueryMgr method) get_variants() (aigct.query.VEBenchmarkQueryMgr method) get_variants_by_task() (aigct.query.VEBenchmarkQueryMgr method)

H

heatmap() (in module aigct.plot_util)

I

include_genes (aigct.model.VEQueryCriteria attribute) include_variant_ids (aigct.model.VEQueryCriteria attribute) init_config_file() (in module aigct.install_util)

init_db() (in module aigct.install_util) init_variant_effect_source() (aigct.etl.repo_loader.RepositoryLoader method) init_variant_task() (aigct.etl.repo_loader.RepositoryLoader method)

L

load_variant_file() (aigct.etl.repo_loader.RepositoryLoader method)

loader (aigct.etl.container.VEETLContainer property)

M

main() (in module aigct.check_install) (in module aigct.init_app) (in module aigct.install_db) merge_by_chunks() (in module aigct.pd_util) MERGE_CHUNK_SIZE (in module aigct.repository) module aigct aigct.analyzer aigct.check_install aigct.config aigct.container aigct.context aigct.date_util aigct.db_model aigct.etl aigct.etl.container aigct.etl.repo_loader aigct.exporter aigct.file_util aigct.init_app aigct.install_db aigct.install_util aigct.model aigct.pd_util aigct.plot_util aigct.plotter aigct.query aigct.query_util aigct.repo_qc aigct.report_util aigct.reporter aigct.repository aigct.util

mwu_metrics (aigct.model.VEAnalysisResult attribute)

N

name (aigct.db_model.VariantEffectSource attribute) (aigct.model.VariantEffectSource attribute) new_line() (in module aigct.file_util) non_pk_columns (aigct.repository.TableDef attribute) now_str_basic_format() (in module aigct.date_util) now_str_compact() (in module aigct.date_util)

num_negative (aigct.db_model.VariantEffectGeneAuc attribute) (aigct.db_model.VariantEffectTaskAuc attribute) num_positive (aigct.db_model.VariantEffectGeneAuc attribute) (aigct.db_model.VariantEffectTaskAuc attribute) num_user_variants (aigct.model.VEAnalysisResult attribute) num_variants_included (aigct.model.VEAnalysisCalibrationResult attribute) (aigct.model.VEAnalysisResult attribute)

P

ParameterizedSingleton (class in aigct.util) pk_columns (aigct.repository.TableDef attribute) PkViolations (class in aigct.model) plot_calibration_curves() (aigct.plotter.VEAnalysisPlotter method) plot_gene_level_results() (aigct.plotter.VEAnalysisPlotter method) plot_gene_results() (aigct.plotter.VEAnalysisPlotter method) plot_mwu_results() (aigct.plotter.VEAnalysisPlotter method)

plot_pr_results() (aigct.plotter.VEAnalysisPlotter method) plot_results() (aigct.plotter.VEAnalysisPlotter method) plot_roc_results() (aigct.plotter.VEAnalysisPlotter method) plotter (aigct.container.VEBenchmarkContainer property) position (aigct.model.VariantId attribute) pr_curve_coordinates (aigct.model.VEAnalysisResult attribute) pr_curve_coordinates_df (aigct.model.VEAnalysisCalibrationResult attribute) pr_metrics (aigct.model.VEAnalysisResult attribute)

Q

query_by_filter() (in module aigct.repository)

query_by_filters() (in module aigct.repository) query_mgr (aigct.container.VEBenchmarkContainer property)

R

read_repo_csv() (in module aigct.repository) reference_nucleotide (aigct.model.VariantId attribute) RELATIONAL_OPERATORS (in module aigct.pd_util) reporter (aigct.container.VEBenchmarkContainer property)

RepoSessionContext (class in aigct.repository) RepositoryLoader (class in aigct.etl.repo_loader) roc_curve_coordinates (aigct.model.VEAnalysisResult attribute) roc_metrics (aigct.model.VEAnalysisResult attribute)

S

sample_user_scores() (in module aigct.install_util) score_pathogenic_fraction_df (aigct.model.VEAnalysisCalibrationResult attribute) score_source (aigct.db_model.VariantEffectGeneAuc attribute) (aigct.db_model.VariantEffectTaskAuc attribute) scores_and_labels_df (aigct.model.VEAnalysisCalibrationResult attribute)

sort_gene_metrics() (aigct.report_util.GeneMetricSorter method) source (aigct.db_model.VariantEffectGeneAuc attribute) (aigct.db_model.VariantEffectTaskAuc attribute) source_type (aigct.db_model.VariantEffectSource attribute) (aigct.model.VariantEffectSource attribute) str_or_list_to_list() (in module aigct.util)

T

table_def() (aigct.repository.RepoSessionContext method) TABLE_DEFS (in module aigct.repository) table_file() (aigct.repository.RepoSessionContext method) TableDef (class in aigct.repository) task_aucs (aigct.db_model.VariantEffectSource attribute) task_code (aigct.db_model.VariantEffectGeneAuc attribute) (aigct.db_model.VariantEffectTaskAuc attribute)

TASK_FOLDERS (in module aigct.repository) TASK_SUBFOLDER (in module aigct.repository) task_violations (aigct.model.PkViolations attribute) TaskBasedDataCache (class in aigct.repository) TaskDataCache (class in aigct.repository) TaskPkViolations (class in aigct.model)

U

unique_file_name() (in module aigct.file_util)

user_vep_name (aigct.model.VEAnalysisResult attribute)

V

validate_pks() (aigct.repo_qc.VEDataValidator method) validate_query_criteria() (in module aigct.query_util) validate_user_ve_scores() (aigct.analyzer.VEAnalyzer method) VARIANT_DATA_SOURCE_DATA (in module aigct.etl.repo_loader) VARIANT_DATA_SOURCE_TABLE_DEF (in module aigct.repository) variant_dups (aigct.model.PkViolations attribute) variant_effect_label_dups (aigct.model.TaskPkViolations attribute) VARIANT_EFFECT_LABEL_TABLE_DEF (in module aigct.repository) VARIANT_EFFECT_SCORE_COLS (in module aigct.analyzer) (in module aigct.reporter) variant_effect_score_dups (aigct.model.TaskPkViolations attribute) VARIANT_EFFECT_SCORE_NON_PK_COLUMNS (in module aigct.repository) VARIANT_EFFECT_SCORE_PK_COLUMNS (in module aigct.repository) VARIANT_EFFECT_SCORE_TABLE_DEF (in module aigct.repository) VARIANT_EFFECT_SOURCE_DATA (in module aigct.etl.repo_loader) variant_effect_source_dups (aigct.model.PkViolations attribute) VARIANT_EFFECT_SOURCE_TABLE_DEF (in module aigct.repository) variant_filter_dups (aigct.model.TaskPkViolations attribute) variant_filter_gene_dups (aigct.model.TaskPkViolations attribute) VARIANT_FILTER_GENE_TABLE_DEF (in module aigct.repository) VARIANT_FILTER_TABLE_DEF (in module aigct.repository) variant_filter_variant_dups (aigct.model.TaskPkViolations attribute) VARIANT_FILTER_VARIANT_TABLE_DEF (in module aigct.repository) variant_ids (aigct.model.VEQueryCriteria attribute) VARIANT_LABEL_NON_PK_COLUMNS (in module aigct.repository) VARIANT_NON_PK_COLUMNS (in module aigct.repository) VARIANT_PK_COLUMNS (in module aigct.repository) VARIANT_TABLE_DEF (in module aigct.repository) VARIANT_TASK_TABLE_DEF (in module aigct.repository) VariantCache (class in aigct.repository) VariantEffectGeneAuc (class in aigct.db_model)

VariantEffectLabelCache (class in aigct.repository) VariantEffectLabelRepository (class in aigct.repository) VariantEffectScoreCache (class in aigct.repository) VariantEffectScoreRepository (class in aigct.repository) VariantEffectSource (class in aigct.db_model) (class in aigct.model) VariantEffectSourceCache (class in aigct.repository) VariantEffectSourceRepository (class in aigct.repository) VariantEffectTaskAuc (class in aigct.db_model) VariantFilter (class in aigct.model) VariantFilterCache (class in aigct.repository) VariantFilterRepository (class in aigct.repository) VariantId (class in aigct.model) VariantRepository (class in aigct.repository) variants_included (aigct.model.VEAnalysisResult attribute) VariantTaskCache (class in aigct.repository) VariantTaskRepository (class in aigct.repository) VEAnalysisCalibrationResult (class in aigct.model) VEAnalysisExporter (class in aigct.exporter) VEAnalysisPlotter (class in aigct.plotter) VEAnalysisReporter (class in aigct.reporter) VEAnalysisResult (class in aigct.model) VEAnalyzer (class in aigct.analyzer) VEBenchmarkContainer (class in aigct.container) VEBenchmarkQueryMgr (class in aigct.query) VEDataValidator (class in aigct.repo_qc) VEETLContainer (class in aigct.etl.container) VEP_COLUMN_LIST (in module aigct.etl.repo_loader) VEP_COLUMN_LIST_OLD (in module aigct.etl.repo_loader) vep_name (aigct.model.VEAnalysisCalibrationResult attribute) VEQueryCriteria (class in aigct.model)

W

write_calibration_summary() (aigct.reporter.VEAnalysisReporter method)

write_summary() (aigct.reporter.VEAnalysisReporter method)