ConStrain package

Sub modules

• Design module
  • Cloning module
    • CAS9_cutting()
    • CRIPSR_knockout()
    • UPandDW()
    • USER_enzyme()
    • casembler()
    • extract_gRNAs()
    • extract_sites()
    • extract_template_amplification_sites()
    • multiply_list()
    • nicking_enzyme()
    • plate_plot()
    • recs_no_duplicates()
    • recs_no_duplicates_names()
    • remove_features_with_negative_loc()
    • remove_tuple_duplicates()
    • seq_to_annotation()
  • Combinatorial library module
    • DesignAssembly
      • DesignAssembly.PCR_list()
      • DesignAssembly.PCR_list_to_dataframe()
      • DesignAssembly.ShowContigs()
      • DesignAssembly.ShowVariantsLibDF()
      • DesignAssembly.graphical_representation_of_assemblies()
      • DesignAssembly.primer_list()
      • DesignAssembly.primer_list_to_dataframe()
      • DesignAssembly.print_PCR_list()
      • DesignAssembly.print_primer_list()
    • assembly_maker()
    • combinatorial_list_maker()
    • count_unique_parts()
    • empty_list_maker()
    • get_primers()
    • making_assembled_contigs()
    • making_assembly_objects()
    • simple_amplicon_maker()
    • systematic_names_function()
    • unique_amplicons()
    • unique_primers()
• Lab module
  • PCR module
    • Q5_NEB_PCR_program()
    • amplicon_by_name()
    • calculate_elongation_time()
    • calculate_processing_speed()
    • calculate_required_thermal_cyclers()
    • calculate_volumes()
    • grouper()
    • nanophotometer_concentrations()
    • pcr_locations()
    • primer_ta_neb()
    • primer_tm_neb()
    • set_plate_locations()
    • update_amplicon_annotations()
  • Containers module
    • NoUniqueWell
    • PickList
      • PickList.add_transfer()
      • PickList.enforce_maximum_dispense_volume()
      • PickList.merge_picklists()
      • PickList.restricted_to()
      • PickList.simulate()
      • PickList.sorted_by()
      • PickList.to_flowbot_instructions_string()
      • PickList.to_plain_string()
      • PickList.to_plain_textfile()
      • PickList.total_transferred_volume()
    • Plate
      • Plate.find_unique_well_by_condition()
      • Plate.find_unique_well_containing()
      • Plate.get_well_at_index()
      • Plate.index_to_wellname()
      • Plate.iter_wells()
      • Plate.list_filtered_wells()
      • Plate.list_well_data_fields()
      • Plate.list_wells_in_column()
      • Plate.list_wells_in_row()
      • Plate.return_column()
      • Plate.return_row()
      • Plate.to_dict()
      • Plate.to_pandas_dataframe()
      • Plate.well_class
      • Plate.wellname_to_index()
      • Plate.wells_grouped_by()
      • Plate.wells_sorted_by()
    • Plate2x4
      • Plate2x4.num_columns
      • Plate2x4.num_rows
    • Plate96
      • Plate96.num_columns
      • Plate96.num_rows
    • Transfer
      • Transfer.apply()
      • Transfer.to_flowbot_instructions()
      • Transfer.to_plain_string()
      • Transfer.to_short_string()
      • Transfer.with_new_volume()
    • TransferError
    • Well
      • Well.add_content()
      • Well.capacity
      • Well.coordinates
      • Well.dead_volume_per_transfer_class
      • Well.empty_completely()
      • Well.index_in_plate()
      • Well.is_after()
      • Well.is_empty
      • Well.iterate_sources_tree()
      • Well.pretty_summary()
      • Well.subtract_content()
      • Well.to_dict()
      • Well.volume
    • WellContent
      • WellContent.components_as_string()
      • WellContent.concentration()
      • WellContent.make_empty()
      • WellContent.to_dict()
    • compute_rows_columns()
    • coordinates_to_wellname()
    • index_to_row_column()
    • index_to_wellname()
    • number_to_rowname()
    • replace_nans_in_dict()
    • rowname_to_number()
    • wellname_to_coordinates()
    • wellname_to_index()
  • Robot assembly module
    • LiquidHandler
      • LiquidHandler.to_flowbot_instructions()
    • RobotAssembly
      • RobotAssembly.FlowbotInstructionsToCSV()
      • RobotAssembly.PlatesToExcelFile()
      • RobotAssembly.print_well_df_to_string()
    • make_virtual_plates_fromDF()
    • picklist_from_plates()
    • well_keys_96()
  • Transformation module
    • ODtime()
    • calculate_volume_and_total_concentration()
    • ng_to_nmol()
    • pool_parts()
    • print_pooled_parts()
    • time_to_inculate()
    • transformation_mix()
    • transformation_partitipants()
    • wanted_mass()
    • wanted_volume()
• LIMS module
  • Benchling API module
    • from_benchling()
    • sequence_to_benchling()
    • session
    • update_loc_vol_conc()
  • CSV database module
    • add_annotations()
    • add_sequences_to_dataframe()
    • add_unique_ids()
    • change_row()
    • delete_row_df()
    • get_box()
    • get_database()
    • get_dna_from_box_name()
    • get_dna_from_plate_name()
    • get_plate()
    • get_unique_id()
    • update_database()
• TEST module
  • Genotyping module
    • concatenating_list_of_dfs()
    • pairwise_alignment_of_templates()
    • plat_seq_data_wrangler()
    • plate_AvgQual()
    • slicing_and_naming_seq_plates()
    • split_df_names()