pmotools.pmo_engine package

Submodules

• pmotools.pmo_engine.pmo_checker module
  • PMOChecker
    • PMOChecker.check_for_required_base_fields()
    • PMOChecker.get_required_fields_for_pmo_class()
    • PMOChecker.validate_pmo_json()
  • load_schema()
  • load_schema_by_version()
• pmotools.pmo_engine.pmo_exporter module
  • BedLoc
    • BedLoc.chrom
    • BedLoc.end
    • BedLoc.extra_info
    • BedLoc.name
    • BedLoc.ref_seq
    • BedLoc.score
    • BedLoc.start
    • BedLoc.strand
  • PMOExporter
    • PMOExporter.SheetConfig
      • PMOExporter.SheetConfig.df
      • PMOExporter.SheetConfig.max_row_check
      • PMOExporter.SheetConfig.sheet_name
      • PMOExporter.SheetConfig.specific_cols
    • PMOExporter.export_bioinformatics_methods_info_meta_table()
    • PMOExporter.export_bioinformatics_run_info_meta_table()
    • PMOExporter.export_library_sample_meta_table()
    • PMOExporter.export_panel_info_meta_table()
    • PMOExporter.export_pmo_header_table()
    • PMOExporter.export_project_info_meta_table()
    • PMOExporter.export_sequencing_info_meta_table()
    • PMOExporter.export_specimen_meta_table()
    • PMOExporter.export_specimen_travel_meta_table()
    • PMOExporter.export_target_info_meta_table()
    • PMOExporter.export_targeted_genomes_meta_table()
    • PMOExporter.export_to_excel()
    • PMOExporter.extract_alleles_per_sample_table()
    • PMOExporter.extract_panels_insert_bed_loc()
    • PMOExporter.extract_targets_insert_bed_loc()
    • PMOExporter.list_library_sample_names_per_specimen_name()
    • PMOExporter.write_bed_locs()
• pmotools.pmo_engine.pmo_processor module
  • PMOProcessor
    • PMOProcessor.count_library_samples_per_target()
    • PMOProcessor.count_specimen_by_field_value()
    • PMOProcessor.count_specimen_per_meta_fields()
    • PMOProcessor.count_targets_per_library_sample()
    • PMOProcessor.count_targets_per_panel()
    • PMOProcessor.extract_allele_counts_freq_from_pmo()
    • PMOProcessor.extract_from_pmo_samples_with_meta_groupings()
    • PMOProcessor.extract_from_pmo_with_read_filter()
    • PMOProcessor.filter_pmo_by_library_sample_ids()
    • PMOProcessor.filter_pmo_by_library_sample_names()
    • PMOProcessor.filter_pmo_by_specimen_ids()
    • PMOProcessor.filter_pmo_by_specimen_names()
    • PMOProcessor.filter_pmo_by_target_ids()
    • PMOProcessor.filter_pmo_by_target_names()
    • PMOProcessor.get_bioinformatics_run_names()
    • PMOProcessor.get_index_key_of_bioinformatics_run_names()
    • PMOProcessor.get_index_key_of_library_sample_names()
    • PMOProcessor.get_index_key_of_panel_names()
    • PMOProcessor.get_index_key_of_specimen_names()
    • PMOProcessor.get_index_key_of_target_in_representative_microhaplotypes()
    • PMOProcessor.get_index_key_of_target_names()
    • PMOProcessor.get_index_of_bioinformatics_run_names()
    • PMOProcessor.get_index_of_library_sample_names()
    • PMOProcessor.get_index_of_panel_names()
    • PMOProcessor.get_index_of_specimen_names()
    • PMOProcessor.get_index_of_target_in_representative_microhaplotypes()
    • PMOProcessor.get_index_of_target_names()
    • PMOProcessor.get_library_ids_for_specimen_ids()
    • PMOProcessor.get_library_sample_names()
    • PMOProcessor.get_panel_names()
    • PMOProcessor.get_sorted_bioinformatics_run_names()
    • PMOProcessor.get_sorted_library_sample_names()
    • PMOProcessor.get_sorted_panel_names()
    • PMOProcessor.get_sorted_specimen_names()
    • PMOProcessor.get_sorted_target_names()
    • PMOProcessor.get_specimen_names()
    • PMOProcessor.get_target_names()
• pmotools.pmo_engine.pmo_reader module
  • PMOReader
    • PMOReader.combine_multiple_pmos()
    • PMOReader.read_in_pmo()
    • PMOReader.read_in_pmos()
• pmotools.pmo_engine.pmo_writer module
  • PMOWriter
    • PMOWriter.add_pmo_extension_as_needed()
    • PMOWriter.write_out_pmo()

Module contents