Index

A

add_parasite_density_info() (in module pmotools.pmo_builder.metatable_to_pmo) add_plate_info() (in module pmotools.pmo_builder.metatable_to_pmo) add_pmo_extension_as_needed() (pmotools.pmo_engine.pmo_writer.PMOWriter static method)

addBGColor() (pmotools.utils.color_text.ColorText static method) addColor() (pmotools.utils.color_text.ColorText static method) appendStrAsNeeded() (pmotools.utils.small_utils.Utils static method) appendStrAsNeededDoubleEnding() (pmotools.utils.small_utils.Utils static method)

B

BedLoc (class in pmotools.pmo_engine.pmo_exporter) black (pmotools.utils.color_text.ColorText attribute) blue (pmotools.utils.color_text.ColorText attribute) bold (pmotools.utils.color_text.ColorText attribute) boldBlack() (pmotools.utils.color_text.ColorText static method) boldBlue() (pmotools.utils.color_text.ColorText static method)

boldGreen() (pmotools.utils.color_text.ColorText static method) boldRed() (pmotools.utils.color_text.ColorText static method) boldText() (pmotools.utils.color_text.ColorText static method) boldWhite() (pmotools.utils.color_text.ColorText static method) build_detected_mhap_dict() (in module pmotools.pmo_builder.mhap_table_to_pmo) build_panel_info_dict() (pmotools.pmo_builder.panel_information_to_pmo.PMOPanelBuilder method) build_target_info_dict() (pmotools.pmo_builder.panel_information_to_pmo.PMOPanelBuilder method)

C

check_additional_columns_exist() (in module pmotools.pmo_builder.json_convert_utils) check_columns_exist() (in module pmotools.pmo_builder.metatable_to_pmo) check_for_required_base_fields() (pmotools.pmo_engine.pmo_checker.PMOChecker method) check_genome_info() (in module pmotools.pmo_builder.panel_information_to_pmo) check_location_columns() (pmotools.pmo_builder.panel_information_to_pmo.PMOPanelBuilder method) check_null_values() (in module pmotools.pmo_builder.json_convert_utils) check_target_names_are_unique() (pmotools.pmo_builder.panel_information_to_pmo.PMOPanelBuilder method) check_unique_columns() (in module pmotools.pmo_builder.metatable_to_pmo) check_unique_target_info() (pmotools.pmo_builder.panel_information_to_pmo.PMOPanelBuilder method) chrom (pmotools.pmo_engine.pmo_exporter.BedLoc attribute) clear_dir() (pmotools.utils.small_utils.Utils static method) ColorText (class in pmotools.utils.color_text) combine_multiple_pmos() (pmotools.pmo_engine.pmo_reader.PMOReader static method)

combine_pmos() (in module pmotools.scripts.pmo_utils.combine_pmos) connectedInternet() (pmotools.utils.small_utils.Utils static method) count_library_samples_per_target() (in module pmotools.scripts.extract_info_from_pmo.count_library_samples_per_target) (pmotools.pmo_engine.pmo_processor.PMOProcessor static method) count_specimen_by_field_value() (pmotools.pmo_engine.pmo_processor.PMOProcessor static method) count_specimen_meta() (in module pmotools.scripts.extract_info_from_pmo.count_specimen_meta) count_specimen_per_meta_fields() (pmotools.pmo_engine.pmo_processor.PMOProcessor static method) count_targets_per_library_sample() (in module pmotools.scripts.extract_info_from_pmo.count_targets_per_library_sample) (pmotools.pmo_engine.pmo_processor.PMOProcessor static method) count_targets_per_panel() (pmotools.pmo_engine.pmo_processor.PMOProcessor static method) create_detected_microhaplotype_dict() (in module pmotools.pmo_builder.mhap_table_to_pmo) create_minimum_library_specimen_dict_from_mhap_table() (in module pmotools.pmo_builder.mhap_table_to_pmo) create_representative_microhaplotype_dict() (in module pmotools.pmo_builder.mhap_table_to_pmo) cyan (pmotools.utils.color_text.ColorText attribute)

D

df (pmotools.pmo_engine.pmo_exporter.PMOExporter.SheetConfig attribute)

E

end (pmotools.pmo_engine.pmo_exporter.BedLoc attribute) excel_meta_to_json_meta() (in module pmotools.scripts.convertors_to_pmo.excel_meta_to_json_meta) export_bioinformatics_methods_info_meta_table() (in module pmotools.scripts.pmo_to_tables.export_bioinformatics_methods_info_meta_table) (pmotools.pmo_engine.pmo_exporter.PMOExporter static method) export_bioinformatics_run_info_meta_table() (in module pmotools.scripts.pmo_to_tables.export_bioinformatics_run_info_meta_table) (pmotools.pmo_engine.pmo_exporter.PMOExporter static method) export_library_sample_meta_table() (in module pmotools.scripts.pmo_to_tables.export_library_sample_meta_table) (pmotools.pmo_engine.pmo_exporter.PMOExporter static method) export_panel_info_meta_table() (in module pmotools.scripts.pmo_to_tables.export_panel_info_meta_table) (pmotools.pmo_engine.pmo_exporter.PMOExporter static method) export_pmo_header_table() (pmotools.pmo_engine.pmo_exporter.PMOExporter static method) export_pmo_into_xlsx() (in module pmotools.scripts.pmo_to_tables.export_pmo_into_xlsx) export_project_info_meta_table() (in module pmotools.scripts.pmo_to_tables.export_project_info_meta_table) (pmotools.pmo_engine.pmo_exporter.PMOExporter static method) export_sequencing_info_meta_table() (in module pmotools.scripts.pmo_to_tables.export_sequencing_info_meta_table) (pmotools.pmo_engine.pmo_exporter.PMOExporter static method) export_specimen_meta_table() (in module pmotools.scripts.pmo_to_tables.export_specimen_meta_table) (pmotools.pmo_engine.pmo_exporter.PMOExporter static method) export_specimen_travel_meta_table() (in module pmotools.scripts.pmo_to_tables.export_specimen_travel_meta_table) (pmotools.pmo_engine.pmo_exporter.PMOExporter static method)

export_target_info_meta_table() (in module pmotools.scripts.pmo_to_tables.export_target_info_meta_table) (pmotools.pmo_engine.pmo_exporter.PMOExporter static method) export_targeted_genomes_meta_table() (in module pmotools.scripts.pmo_to_tables.export_targeted_genomes_meta_table) (pmotools.pmo_engine.pmo_exporter.PMOExporter static method) export_to_excel() (pmotools.pmo_engine.pmo_exporter.PMOExporter static method) extra_info (pmotools.pmo_engine.pmo_exporter.BedLoc attribute) extract_allele_counts_freq_from_pmo() (pmotools.pmo_engine.pmo_processor.PMOProcessor static method) extract_alleles_per_sample_table() (pmotools.pmo_engine.pmo_exporter.PMOExporter static method) extract_for_allele_table() (in module pmotools.scripts.pmo_to_tables.extract_allele_table) extract_from_pmo_samples_with_meta_groupings() (pmotools.pmo_engine.pmo_processor.PMOProcessor static method) extract_from_pmo_with_read_filter() (pmotools.pmo_engine.pmo_processor.PMOProcessor static method) extract_insert_of_panels() (in module pmotools.scripts.pmo_to_tables.extract_insert_of_panels) extract_panels_insert_bed_loc() (pmotools.pmo_engine.pmo_exporter.PMOExporter static method) extract_pmo_with_read_filter() (in module pmotools.scripts.extractors_from_pmo.extract_pmo_with_read_filter) extract_pmo_with_select_library_sample_names() (in module pmotools.scripts.extractors_from_pmo.extract_pmo_with_select_library_sample_names) extract_pmo_with_select_specimen_names() (in module pmotools.scripts.extractors_from_pmo.extract_pmo_with_select_specimen_names) extract_pmo_with_select_targets() (in module pmotools.scripts.extractors_from_pmo.extract_pmo_with_select_targets) extract_pmo_with_selected_meta() (in module pmotools.scripts.extractors_from_pmo.extract_pmo_with_selected_meta) extract_refseq_of_inserts_of_panels() (in module pmotools.scripts.pmo_to_tables.extract_refseq_of_inserts_of_panels) extract_targets_insert_bed_loc() (pmotools.pmo_engine.pmo_exporter.PMOExporter static method)

F

filter_pmo_by_library_sample_ids() (pmotools.pmo_engine.pmo_processor.PMOProcessor static method) filter_pmo_by_library_sample_names() (pmotools.pmo_engine.pmo_processor.PMOProcessor static method) filter_pmo_by_specimen_ids() (pmotools.pmo_engine.pmo_processor.PMOProcessor static method) filter_pmo_by_specimen_names() (pmotools.pmo_engine.pmo_processor.PMOProcessor static method)

filter_pmo_by_target_ids() (pmotools.pmo_engine.pmo_processor.PMOProcessor static method) filter_pmo_by_target_names() (pmotools.pmo_engine.pmo_processor.PMOProcessor static method) flashing (pmotools.utils.color_text.ColorText attribute) func (pmotools.cli.PmoCommand attribute)

G

get_bioinformatics_run_names() (pmotools.pmo_engine.pmo_processor.PMOProcessor static method) get_file() (pmotools.utils.small_utils.Utils static method) get_file_if_size_diff() (pmotools.utils.small_utils.Utils static method) get_index_key_of_bioinformatics_run_names() (pmotools.pmo_engine.pmo_processor.PMOProcessor static method) get_index_key_of_library_sample_names() (pmotools.pmo_engine.pmo_processor.PMOProcessor static method) get_index_key_of_panel_names() (pmotools.pmo_engine.pmo_processor.PMOProcessor static method) get_index_key_of_specimen_names() (pmotools.pmo_engine.pmo_processor.PMOProcessor static method) get_index_key_of_target_in_representative_microhaplotypes() (pmotools.pmo_engine.pmo_processor.PMOProcessor static method) get_index_key_of_target_names() (pmotools.pmo_engine.pmo_processor.PMOProcessor static method) get_index_of_bioinformatics_run_names() (pmotools.pmo_engine.pmo_processor.PMOProcessor static method) get_index_of_library_sample_names() (pmotools.pmo_engine.pmo_processor.PMOProcessor static method) get_index_of_panel_names() (pmotools.pmo_engine.pmo_processor.PMOProcessor static method) get_index_of_specimen_names() (pmotools.pmo_engine.pmo_processor.PMOProcessor static method) get_index_of_target_in_representative_microhaplotypes() (pmotools.pmo_engine.pmo_processor.PMOProcessor static method) get_index_of_target_names() (pmotools.pmo_engine.pmo_processor.PMOProcessor static method) get_library_ids_for_specimen_ids() (pmotools.pmo_engine.pmo_processor.PMOProcessor static method) get_library_sample_names() (pmotools.pmo_engine.pmo_processor.PMOProcessor static method) get_mhap_index_in_representative_mhaps() (in module pmotools.pmo_builder.mhap_table_to_pmo) get_panel_names() (pmotools.pmo_engine.pmo_processor.PMOProcessor static method) get_parser() (in module pmotools.scripts.pmo_to_tables.extract_allele_table) get_parser_combine_pmos() (in module pmotools.scripts.pmo_utils.combine_pmos) get_parser_count_library_samples_per_target() (in module pmotools.scripts.extract_info_from_pmo.count_library_samples_per_target) get_parser_count_specimen_meta() (in module pmotools.scripts.extract_info_from_pmo.count_specimen_meta) get_parser_count_targets_per_library_sample() (in module pmotools.scripts.extract_info_from_pmo.count_targets_per_library_sample) get_parser_excel_meta_to_json_meta() (in module pmotools.scripts.convertors_to_pmo.excel_meta_to_json_meta) get_parser_export_bioinformatics_methods_info_meta_table() (in module pmotools.scripts.pmo_to_tables.export_bioinformatics_methods_info_meta_table) get_parser_export_bioinformatics_run_info_meta_table() (in module pmotools.scripts.pmo_to_tables.export_bioinformatics_run_info_meta_table) get_parser_export_library_sample_meta_table() (in module pmotools.scripts.pmo_to_tables.export_library_sample_meta_table) get_parser_export_panel_info_meta_table() (in module pmotools.scripts.pmo_to_tables.export_panel_info_meta_table) get_parser_export_pmo_into_xlsx() (in module pmotools.scripts.pmo_to_tables.export_pmo_into_xlsx) get_parser_export_project_info_meta_table() (in module pmotools.scripts.pmo_to_tables.export_project_info_meta_table)

get_parser_export_sequencing_info_meta_table() (in module pmotools.scripts.pmo_to_tables.export_sequencing_info_meta_table) get_parser_export_specimen_meta_table() (in module pmotools.scripts.pmo_to_tables.export_specimen_meta_table) get_parser_export_specimen_travel_meta_table() (in module pmotools.scripts.pmo_to_tables.export_specimen_travel_meta_table) get_parser_export_target_info_meta_table() (in module pmotools.scripts.pmo_to_tables.export_target_info_meta_table) get_parser_export_targeted_genomes_meta_table() (in module pmotools.scripts.pmo_to_tables.export_targeted_genomes_meta_table) get_parser_extract_insert_of_panels() (in module pmotools.scripts.pmo_to_tables.extract_insert_of_panels) get_parser_extract_pmo_with_read_filter() (in module pmotools.scripts.extractors_from_pmo.extract_pmo_with_read_filter) get_parser_extract_pmo_with_select_library_sample_names() (in module pmotools.scripts.extractors_from_pmo.extract_pmo_with_select_library_sample_names) get_parser_extract_pmo_with_select_specimen_names() (in module pmotools.scripts.extractors_from_pmo.extract_pmo_with_select_specimen_names) get_parser_extract_pmo_with_select_targets() (in module pmotools.scripts.extractors_from_pmo.extract_pmo_with_select_targets) get_parser_extract_pmo_with_selected_meta() (in module pmotools.scripts.extractors_from_pmo.extract_pmo_with_selected_meta) get_parser_extract_refseq_of_inserts_of_panels() (in module pmotools.scripts.pmo_to_tables.extract_refseq_of_inserts_of_panels) get_parser_list_bioinformatics_run_names() (in module pmotools.scripts.extract_info_from_pmo.list_bioinformatics_run_names) get_parser_list_library_sample_names_per_specimen_name() (in module pmotools.scripts.extract_info_from_pmo.list_library_sample_names_per_specimen_name) get_parser_list_specimen_meta_fields() (in module pmotools.scripts.extract_info_from_pmo.list_specimen_meta_fields) get_parser_microhaplotype_table_to_json_file() (in module pmotools.scripts.convertors_to_pmo.microhaplotype_table_to_json_file) get_parser_terra_amp_output_to_json() (in module pmotools.scripts.convertors_to_pmo.terra_amp_output_to_json) get_parser_text_meta_to_json_meta() (in module pmotools.scripts.convertors_to_pmo.text_meta_to_json_meta) get_parser_validate_pmo() (in module pmotools.scripts.pmo_utils.validate_pmo) get_pmo_schema_version() (in module pmotools) get_pmotools_version() (in module pmotools) get_required_fields_for_pmo_class() (pmotools.pmo_engine.pmo_checker.PMOChecker method) get_sorted_bioinformatics_run_names() (pmotools.pmo_engine.pmo_processor.PMOProcessor static method) get_sorted_library_sample_names() (pmotools.pmo_engine.pmo_processor.PMOProcessor static method) get_sorted_panel_names() (pmotools.pmo_engine.pmo_processor.PMOProcessor static method) get_sorted_specimen_names() (pmotools.pmo_engine.pmo_processor.PMOProcessor static method) get_sorted_target_names() (pmotools.pmo_engine.pmo_processor.PMOProcessor static method) get_specimen_names() (pmotools.pmo_engine.pmo_processor.PMOProcessor static method) get_target_id_in_representative_mhaps() (in module pmotools.pmo_builder.mhap_table_to_pmo) get_target_names() (pmotools.pmo_engine.pmo_processor.PMOProcessor static method) getStrFromStrOrList() (pmotools.utils.small_utils.Utils static method) green (pmotools.utils.color_text.ColorText attribute)

H

hasProgram() (pmotools.utils.small_utils.Utils static method)

help (pmotools.cli.PmoCommand attribute)

I

iBlack (pmotools.utils.color_text.ColorText attribute) iBlue (pmotools.utils.color_text.ColorText attribute) iCyan (pmotools.utils.color_text.ColorText attribute) iGreen (pmotools.utils.color_text.ColorText attribute) inputOutputFileCheck() (pmotools.utils.small_utils.Utils static method) inputOutputFileCheckFromArgParse() (pmotools.utils.small_utils.Utils static method)

invert (pmotools.utils.color_text.ColorText attribute) iPurple (pmotools.utils.color_text.ColorText attribute) iRed (pmotools.utils.color_text.ColorText attribute) isMac() (pmotools.utils.small_utils.Utils static method) iWhite (pmotools.utils.color_text.ColorText attribute) iYellow (pmotools.utils.color_text.ColorText attribute)

L

library_sample_info_table_to_pmo() (in module pmotools.pmo_builder.metatable_to_pmo) lighten (pmotools.utils.color_text.ColorText attribute) list_bioinformatics_run_names() (in module pmotools.scripts.extract_info_from_pmo.list_bioinformatics_run_names) list_library_sample_names_per_specimen_name() (in module pmotools.scripts.extract_info_from_pmo.list_library_sample_names_per_specimen_name) (pmotools.pmo_engine.pmo_exporter.PMOExporter static method)

list_specimen_meta_fields() (in module pmotools.scripts.extract_info_from_pmo.list_specimen_meta_fields) load_schema() (in module pmotools.pmo_engine.pmo_checker) load_schema_by_version() (in module pmotools.pmo_engine.pmo_checker)

M

main() (in module pmotools.cli) max_row_check (pmotools.pmo_engine.pmo_exporter.PMOExporter.SheetConfig attribute) merge_dicts_by_key() (pmotools.pmo_builder.pmo_updater.PMOUpdater static method) merge_panel_info_dicts() (in module pmotools.pmo_builder.panel_information_to_pmo) merge_to_pmo() (in module pmotools.pmo_builder.merge_to_pmo) mhap_table_to_pmo() (in module pmotools.pmo_builder.mhap_table_to_pmo) microhaplotype_table_to_json_file() (in module pmotools.scripts.convertors_to_pmo.microhaplotype_table_to_json_file) mkdir() (pmotools.utils.small_utils.Utils static method) module pmotools pmotools.cli pmotools.pmo_builder pmotools.pmo_builder.json_convert_utils pmotools.pmo_builder.merge_to_pmo pmotools.pmo_builder.metatable_to_pmo pmotools.pmo_builder.mhap_table_to_pmo pmotools.pmo_builder.panel_information_to_pmo pmotools.pmo_builder.pmo_updater pmotools.pmo_builder.read_count_by_stage_table_to_pmo pmotools.pmo_engine pmotools.pmo_engine.pmo_checker pmotools.pmo_engine.pmo_exporter pmotools.pmo_engine.pmo_processor pmotools.pmo_engine.pmo_reader pmotools.pmo_engine.pmo_writer pmotools.scripts pmotools.scripts.convertors_to_pmo pmotools.scripts.convertors_to_pmo.excel_meta_to_json_meta pmotools.scripts.convertors_to_pmo.microhaplotype_table_to_json_file pmotools.scripts.convertors_to_pmo.terra_amp_output_to_json pmotools.scripts.convertors_to_pmo.text_meta_to_json_meta pmotools.scripts.extract_info_from_pmo pmotools.scripts.extract_info_from_pmo.count_library_samples_per_target pmotools.scripts.extract_info_from_pmo.count_specimen_meta pmotools.scripts.extract_info_from_pmo.count_targets_per_library_sample pmotools.scripts.extract_info_from_pmo.list_bioinformatics_run_names pmotools.scripts.extract_info_from_pmo.list_library_sample_names_per_specimen_name pmotools.scripts.extract_info_from_pmo.list_specimen_meta_fields pmotools.scripts.extractors_from_pmo pmotools.scripts.extractors_from_pmo.extract_pmo_with_read_filter pmotools.scripts.extractors_from_pmo.extract_pmo_with_select_library_sample_names pmotools.scripts.extractors_from_pmo.extract_pmo_with_select_specimen_names pmotools.scripts.extractors_from_pmo.extract_pmo_with_select_targets pmotools.scripts.extractors_from_pmo.extract_pmo_with_selected_meta pmotools.scripts.pmo_to_tables pmotools.scripts.pmo_to_tables.export_bioinformatics_methods_info_meta_table pmotools.scripts.pmo_to_tables.export_bioinformatics_run_info_meta_table pmotools.scripts.pmo_to_tables.export_library_sample_meta_table pmotools.scripts.pmo_to_tables.export_panel_info_meta_table pmotools.scripts.pmo_to_tables.export_pmo_into_xlsx pmotools.scripts.pmo_to_tables.export_project_info_meta_table pmotools.scripts.pmo_to_tables.export_sequencing_info_meta_table pmotools.scripts.pmo_to_tables.export_specimen_meta_table pmotools.scripts.pmo_to_tables.export_specimen_travel_meta_table pmotools.scripts.pmo_to_tables.export_target_info_meta_table pmotools.scripts.pmo_to_tables.export_targeted_genomes_meta_table pmotools.scripts.pmo_to_tables.extract_allele_table pmotools.scripts.pmo_to_tables.extract_insert_of_panels pmotools.scripts.pmo_to_tables.extract_refseq_of_inserts_of_panels pmotools.scripts.pmo_utils pmotools.scripts.pmo_utils.combine_pmos pmotools.scripts.pmo_utils.validate_pmo pmotools.utils pmotools.utils.color_text pmotools.utils.small_utils

N

name (pmotools.pmo_engine.pmo_exporter.BedLoc attribute)

num_cores() (pmotools.utils.small_utils.Utils static method)

O

on_Black (pmotools.utils.color_text.ColorText attribute) on_Blue (pmotools.utils.color_text.ColorText attribute) on_Cyan (pmotools.utils.color_text.ColorText attribute) on_Green (pmotools.utils.color_text.ColorText attribute) on_IBlack (pmotools.utils.color_text.ColorText attribute) on_IBlue (pmotools.utils.color_text.ColorText attribute) on_ICyan (pmotools.utils.color_text.ColorText attribute) on_IGreen (pmotools.utils.color_text.ColorText attribute) on_IPurple (pmotools.utils.color_text.ColorText attribute)

on_IRed (pmotools.utils.color_text.ColorText attribute) on_IWhite (pmotools.utils.color_text.ColorText attribute) on_IYellow (pmotools.utils.color_text.ColorText attribute) on_Purple (pmotools.utils.color_text.ColorText attribute) on_Red (pmotools.utils.color_text.ColorText attribute) on_White (pmotools.utils.color_text.ColorText attribute) on_Yellow (pmotools.utils.color_text.ColorText attribute) outputColors() (pmotools.utils.color_text.ColorText static method) outputfile_check() (pmotools.utils.small_utils.Utils static method)

P

pandas_table_to_json() (in module pmotools.pmo_builder.metatable_to_pmo) panel_info_table_to_pmo() (in module pmotools.pmo_builder.panel_information_to_pmo) parse_args_combine_pmos() (in module pmotools.scripts.pmo_utils.combine_pmos) parse_args_count_library_samples_per_target() (in module pmotools.scripts.extract_info_from_pmo.count_library_samples_per_target) parse_args_count_specimen_meta() (in module pmotools.scripts.extract_info_from_pmo.count_specimen_meta) parse_args_count_targets_per_library_sample() (in module pmotools.scripts.extract_info_from_pmo.count_targets_per_library_sample) parse_args_excel_meta_to_json_meta() (in module pmotools.scripts.convertors_to_pmo.excel_meta_to_json_meta) parse_args_export_bioinformatics_methods_info_meta_table() (in module pmotools.scripts.pmo_to_tables.export_bioinformatics_methods_info_meta_table) parse_args_export_bioinformatics_run_info_meta_table() (in module pmotools.scripts.pmo_to_tables.export_bioinformatics_run_info_meta_table) parse_args_export_library_sample_meta_table() (in module pmotools.scripts.pmo_to_tables.export_library_sample_meta_table) parse_args_export_panel_info_meta_table() (in module pmotools.scripts.pmo_to_tables.export_panel_info_meta_table) parse_args_export_pmo_into_xlsx() (in module pmotools.scripts.pmo_to_tables.export_pmo_into_xlsx) parse_args_export_project_info_meta_table() (in module pmotools.scripts.pmo_to_tables.export_project_info_meta_table) parse_args_export_sequencing_info_meta_table() (in module pmotools.scripts.pmo_to_tables.export_sequencing_info_meta_table) parse_args_export_specimen_meta_table() (in module pmotools.scripts.pmo_to_tables.export_specimen_meta_table) parse_args_export_specimen_travel_meta_table() (in module pmotools.scripts.pmo_to_tables.export_specimen_travel_meta_table) parse_args_export_target_info_meta_table() (in module pmotools.scripts.pmo_to_tables.export_target_info_meta_table) parse_args_export_targeted_genomes_meta_table() (in module pmotools.scripts.pmo_to_tables.export_targeted_genomes_meta_table) parse_args_extract_for_allele_table() (in module pmotools.scripts.pmo_to_tables.extract_allele_table) parse_args_extract_insert_of_panels() (in module pmotools.scripts.pmo_to_tables.extract_insert_of_panels) parse_args_extract_pmo_with_read_filter() (in module pmotools.scripts.extractors_from_pmo.extract_pmo_with_read_filter) parse_args_extract_pmo_with_select_library_sample_names() (in module pmotools.scripts.extractors_from_pmo.extract_pmo_with_select_library_sample_names) parse_args_extract_pmo_with_select_specimen_names() (in module pmotools.scripts.extractors_from_pmo.extract_pmo_with_select_specimen_names) parse_args_extract_pmo_with_select_targets() (in module pmotools.scripts.extractors_from_pmo.extract_pmo_with_select_targets) parse_args_extract_pmo_with_selected_meta() (in module pmotools.scripts.extractors_from_pmo.extract_pmo_with_selected_meta) parse_args_extract_refseq_of_inserts_of_panels() (in module pmotools.scripts.pmo_to_tables.extract_refseq_of_inserts_of_panels) parse_args_list_bioinformatics_run_names() (in module pmotools.scripts.extract_info_from_pmo.list_bioinformatics_run_names) parse_args_list_library_sample_names_per_specimen_name() (in module pmotools.scripts.extract_info_from_pmo.list_library_sample_names_per_specimen_name) parse_args_list_specimen_meta_fields() (in module pmotools.scripts.extract_info_from_pmo.list_specimen_meta_fields) parse_args_microhaplotype_table_to_json_file() (in module pmotools.scripts.convertors_to_pmo.microhaplotype_table_to_json_file) parse_args_terra_amp_output_to_json() (in module pmotools.scripts.convertors_to_pmo.terra_amp_output_to_json) parse_args_text_meta_to_json_meta() (in module pmotools.scripts.convertors_to_pmo.text_meta_to_json_meta) parse_args_validate_pmo() (in module pmotools.scripts.pmo_utils.validate_pmo) parse_delimited_input_or_file() (pmotools.utils.small_utils.Utils static method) PMOChecker (class in pmotools.pmo_engine.pmo_checker) PmoCommand (class in pmotools.cli) PMOExporter (class in pmotools.pmo_engine.pmo_exporter) PMOExporter.SheetConfig (class in pmotools.pmo_engine.pmo_exporter) PMOPanelBuilder (class in pmotools.pmo_builder.panel_information_to_pmo) PMOProcessor (class in pmotools.pmo_engine.pmo_processor) PMOReader (class in pmotools.pmo_engine.pmo_reader) pmotools module pmotools.cli module pmotools.pmo_builder module pmotools.pmo_builder.json_convert_utils module pmotools.pmo_builder.merge_to_pmo module pmotools.pmo_builder.metatable_to_pmo module pmotools.pmo_builder.mhap_table_to_pmo module pmotools.pmo_builder.panel_information_to_pmo module pmotools.pmo_builder.pmo_updater module pmotools.pmo_builder.read_count_by_stage_table_to_pmo module pmotools.pmo_engine module pmotools.pmo_engine.pmo_checker module pmotools.pmo_engine.pmo_exporter module pmotools.pmo_engine.pmo_processor module pmotools.pmo_engine.pmo_reader module pmotools.pmo_engine.pmo_writer module pmotools.scripts module pmotools.scripts.convertors_to_pmo module pmotools.scripts.convertors_to_pmo.excel_meta_to_json_meta module

pmotools.scripts.convertors_to_pmo.microhaplotype_table_to_json_file module pmotools.scripts.convertors_to_pmo.terra_amp_output_to_json module pmotools.scripts.convertors_to_pmo.text_meta_to_json_meta module pmotools.scripts.extract_info_from_pmo module pmotools.scripts.extract_info_from_pmo.count_library_samples_per_target module pmotools.scripts.extract_info_from_pmo.count_specimen_meta module pmotools.scripts.extract_info_from_pmo.count_targets_per_library_sample module pmotools.scripts.extract_info_from_pmo.list_bioinformatics_run_names module pmotools.scripts.extract_info_from_pmo.list_library_sample_names_per_specimen_name module pmotools.scripts.extract_info_from_pmo.list_specimen_meta_fields module pmotools.scripts.extractors_from_pmo module pmotools.scripts.extractors_from_pmo.extract_pmo_with_read_filter module pmotools.scripts.extractors_from_pmo.extract_pmo_with_select_library_sample_names module pmotools.scripts.extractors_from_pmo.extract_pmo_with_select_specimen_names module pmotools.scripts.extractors_from_pmo.extract_pmo_with_select_targets module pmotools.scripts.extractors_from_pmo.extract_pmo_with_selected_meta module pmotools.scripts.pmo_to_tables module pmotools.scripts.pmo_to_tables.export_bioinformatics_methods_info_meta_table module pmotools.scripts.pmo_to_tables.export_bioinformatics_run_info_meta_table module pmotools.scripts.pmo_to_tables.export_library_sample_meta_table module pmotools.scripts.pmo_to_tables.export_panel_info_meta_table module pmotools.scripts.pmo_to_tables.export_pmo_into_xlsx module pmotools.scripts.pmo_to_tables.export_project_info_meta_table module pmotools.scripts.pmo_to_tables.export_sequencing_info_meta_table module pmotools.scripts.pmo_to_tables.export_specimen_meta_table module pmotools.scripts.pmo_to_tables.export_specimen_travel_meta_table module pmotools.scripts.pmo_to_tables.export_target_info_meta_table module pmotools.scripts.pmo_to_tables.export_targeted_genomes_meta_table module pmotools.scripts.pmo_to_tables.extract_allele_table module pmotools.scripts.pmo_to_tables.extract_insert_of_panels module pmotools.scripts.pmo_to_tables.extract_refseq_of_inserts_of_panels module pmotools.scripts.pmo_utils module pmotools.scripts.pmo_utils.combine_pmos module pmotools.scripts.pmo_utils.validate_pmo module pmotools.utils module pmotools.utils.color_text module pmotools.utils.small_utils module PMOUpdater (class in pmotools.pmo_builder.pmo_updater) PMOWriter (class in pmotools.pmo_engine.pmo_writer) process_delimiter_and_output_extension() (pmotools.utils.small_utils.Utils static method) purple (pmotools.utils.color_text.ColorText attribute)

R

read_count_by_stage_table_to_pmo() (in module pmotools.pmo_builder.read_count_by_stage_table_to_pmo) read_in_pmo() (pmotools.pmo_engine.pmo_reader.PMOReader static method) read_in_pmos() (pmotools.pmo_engine.pmo_reader.PMOReader static method) red (pmotools.utils.color_text.ColorText attribute) ref_seq (pmotools.pmo_engine.pmo_exporter.BedLoc attribute)

remove_optional_null_values() (in module pmotools.pmo_builder.json_convert_utils) reset (pmotools.utils.color_text.ColorText attribute) rm_rf() (pmotools.utils.small_utils.Utils static method) run() (pmotools.utils.small_utils.Utils static method) run_in_dir() (pmotools.utils.small_utils.Utils static method) runAndCapture() (pmotools.utils.small_utils.Utils static method)

S

score (pmotools.pmo_engine.pmo_exporter.BedLoc attribute) sheet_name (pmotools.pmo_engine.pmo_exporter.PMOExporter.SheetConfig attribute) shellquote() (pmotools.utils.small_utils.Utils static method) smart_open_read_autodetect() (pmotools.utils.small_utils.Utils static method) smart_open_read_by_ext() (pmotools.utils.small_utils.Utils static method)

smart_open_write() (pmotools.utils.small_utils.Utils static method) specific_cols (pmotools.pmo_engine.pmo_exporter.PMOExporter.SheetConfig attribute) specimen_info_table_to_pmo() (in module pmotools.pmo_builder.metatable_to_pmo) start (pmotools.pmo_engine.pmo_exporter.BedLoc attribute) strand (pmotools.pmo_engine.pmo_exporter.BedLoc attribute) summarise_targets_missing_optional_info() (pmotools.pmo_builder.panel_information_to_pmo.PMOPanelBuilder method)

T

terra_amp_output_to_json() (in module pmotools.scripts.convertors_to_pmo.terra_amp_output_to_json)

text_meta_to_json_meta() (in module pmotools.scripts.convertors_to_pmo.text_meta_to_json_meta)

U

underline (pmotools.utils.color_text.ColorText attribute) untar() (pmotools.utils.small_utils.Utils static method)

update_specimen_meta_with_traveler_info() (pmotools.pmo_builder.pmo_updater.PMOUpdater static method) Utils (class in pmotools.utils.small_utils)

V

validate_pmo() (in module pmotools.scripts.pmo_utils.validate_pmo)

validate_pmo_json() (pmotools.pmo_engine.pmo_checker.PMOChecker method)

W

which() (pmotools.utils.small_utils.Utils static method) white (pmotools.utils.color_text.ColorText attribute)

write_bed_locs() (pmotools.pmo_engine.pmo_exporter.PMOExporter static method) write_out_pmo() (pmotools.pmo_engine.pmo_writer.PMOWriter static method)

Y

yellow (pmotools.utils.color_text.ColorText attribute)