pmotools package

Subpackages

• pmotools.pmo_builder package
  • Submodules
    • pmotools.pmo_builder.json_convert_utils module
      • check_additional_columns_exist()
      • check_null_values()
      • remove_optional_null_values()
    • pmotools.pmo_builder.merge_to_pmo module
      • merge_to_pmo()
    • pmotools.pmo_builder.metatable_to_pmo module
      • add_parasite_density_info()
      • add_plate_info()
      • check_columns_exist()
      • check_unique_columns()
      • library_sample_info_table_to_pmo()
      • pandas_table_to_json()
      • specimen_info_table_to_pmo()
    • pmotools.pmo_builder.mhap_table_to_pmo module
      • build_detected_mhap_dict()
      • create_detected_microhaplotype_dict()
      • create_minimum_library_specimen_dict_from_mhap_table()
      • create_representative_microhaplotype_dict()
      • get_mhap_index_in_representative_mhaps()
      • get_target_id_in_representative_mhaps()
      • mhap_table_to_pmo()
    • pmotools.pmo_builder.panel_information_to_pmo module
      • PMOPanelBuilder
      • check_genome_info()
      • merge_panel_info_dicts()
      • panel_info_table_to_pmo()
    • pmotools.pmo_builder.pmo_updater module
      • PMOUpdater
    • pmotools.pmo_builder.read_count_by_stage_table_to_pmo module
      • read_count_by_stage_table_to_pmo()
  • Module contents
• pmotools.pmo_engine package
  • Submodules
    • pmotools.pmo_engine.pmo_checker module
      • PMOChecker
      • load_schema()
      • load_schema_by_version()
    • pmotools.pmo_engine.pmo_exporter module
      • BedLoc
      • PMOExporter
    • pmotools.pmo_engine.pmo_processor module
      • PMOProcessor
    • pmotools.pmo_engine.pmo_reader module
      • PMOReader
    • pmotools.pmo_engine.pmo_writer module
      • PMOWriter
  • Module contents
• pmotools.scripts package
  • Subpackages
    • pmotools.scripts.convertors_to_pmo package
      • Submodules
      • Module contents
    • pmotools.scripts.extract_info_from_pmo package
      • Submodules
      • Module contents
    • pmotools.scripts.extractors_from_pmo package
      • Submodules
      • Module contents
    • pmotools.scripts.pmo_to_tables package
      • Submodules
      • Module contents
    • pmotools.scripts.pmo_utils package
      • Submodules
      • Module contents
  • Module contents
• pmotools.utils package
  • Submodules
    • pmotools.utils.color_text module
      • ColorText
    • pmotools.utils.small_utils module
      • Utils
  • Module contents

Submodules

• pmotools.cli module
  • PmoCommand
    • PmoCommand.func
    • PmoCommand.help
  • main()

Module contents

pmotools.get_pmo_schema_version() → str

Return the PMO schema version this package targets (e.g. ‘1.0.0’).

pmotools.get_pmotools_version() → str

Return the installed pmotools package version (e.g. ‘1.0.0’).