moclo_assembly.moclo_transformation.moclo_transform_generator

moclo_function

moclo_function(output_folder: str, construct_path: List[str], part_path: List[str], thermocycle: bool = True, p10_mount: str = 'right', p300_mount: str = 'left', p10_type: str = 'p10_single', p300_type: str = 'p300_multi', well_plate: str = 'biorad_96_wellplate_200ul_pcr', trough: str = 'usascientific_12_reservoir_22ml', reagent_plate: str = 'biorad_96_wellplate_200ul_pcr', agar_plate: str = 'thermofisher_96_wellplate_180ul') -> List[str]

Main function, creates scripts and metainformation Can take specific args or just **labware_dict for all labware

Arguments:

  • output_folder - the full file path of the intended output folder for files generated
  • construct_path - a one element list with the full path of the construct csv
  • part_path - a list of full paths to part csv(s) (one or more)
  • thermocyle - True or False, indicating whether the user has and would like to use the Opentrons Thermocycler see labware_dict for rest of arguments

Returns:

List of output paths If there is an exception, the list of output paths will contain only one element = the error path Otherwise the list of output paths will contain: OT-2 script paths (assembly, transformation), metainformation (assembly, transformation, agar plate)

generate_plate_maps

generate_plate_maps(filename: str) -> Dict[str, List[List]]

Generates dictionaries for the part csvs Args: filename = absolute path to part csv Returns: dictionary of plate maps with key = name of part csv, value = list of rows (= list of lists)

generate_combinations

generate_combinations(combinations_filename: str) -> List[Dict]

Generates a list of dictionaries of constructs to be made Args: combinations_filename = absolute path to construct csv file Returns: List of construct dictionaries with keys "name" and "parts"

check_number_of_combinations

check_number_of_combinations(combinations_limit: str, combinations_to_make: List[Dict])

Ensures that the number of constructs does not exceed the maximum

Arguments:

  • combinations_limit - "single" or "triplicate" - if "single" can do max 88 constructs, if "triplicate" does every construct 3 times - max 24 constructs
  • Raises - ValueError if there are too many constructs or combinations_limit is not "single" or "triplicate"

generate_and_save_output_plate_maps

generate_and_save_output_plate_maps(combinations_to_make: List[Dict], combinations_limit: str, output_folder_path: str) -> Tuple[str, str]

Saves the mapping of the agar plate for use in transformation.

Arguments:

combinations_to_make = list of construct dictionaries combinations_limit = "single" or "triplicate" output_folder_path = where to save mapping

Returns:

  • triplicate - whether 'single' (triplicate = False) or 'triplicate' (triplicate = True) is selected
  • output_filename - the absolute path to the agar plate csv

create_metainformation

create_metainformation(output_path: str, dna_plate_map_dict: Dict[str, List[List]], combinations_to_make: List[Dict], labware_dict: Dict[str, str], thermocycle: bool, triplicate: str) -> Tuple[pd.DataFrame, pd.DataFrame, pd.DataFrame, pd.DataFrame]

Returns detailed metainformation and saves in a csv. Includes a parts dataframe, a combinations (constructs) dataframe, a reagents dataframe, and a master mix dataframe.

Arguments:

  • output_path - the full path of the output folder
  • dna_plate_map_dict - the dictionary of parts
  • combinations_to_make - the list of dictionaries of constructs
  • labware_dict - the dictionary of labware chosen
  • thermocyle - whether the thermocycler module is used
  • triplicate - whether 'single' (triplicate = False) or 'triplicate' (triplicate = True) is selected

Returns:

  • parts_df - dataframe of parts
  • combinations_df - dataframe of constructs
  • mm_df - master mix dataframe, contains information on all of the master mixes needed (different master mix needed for different number of parts per construct)
  • reagents_df - reagents dataframe, contains information on all of the reagents, does not include master mix but DOES include reagents to go into master mixes

create_parts_df

create_parts_df(dna_plate_map_dict: Dict[str, List[List]]) -> pd.DataFrame

Returns a dataframe of parts and delegates wells. Takes in the dictionary of parts.

Arguments:

  • dna_plate_map_dict - dictionary with keys = plate names, values = list of rows = list of list of parts

Returns:

  • parts_df - dataframe of parts with dummy '0' for combinations col

create_mm_df

create_mm_df(combinations_df: pd.DataFrame) -> pd.DataFrame

Creates a master mix dataframe and delegates wells. Different master mixes must be created depending on the number of parts per construct. Args: combinations_df = dataframe of constructs Returns: dataframe of master mixes with wells and volumes of different reagents required

create_reagents_df

create_reagents_df(mm_df: pd.DataFrame) -> pd.DataFrame

Creates a dataframe of reagents used to make master mixes. More than one buffer well may be required, and water is held on a separate plate. Also indicates which master mix wells the reagent is transferred to. Args: master mix dataframe Returns: dataframe of reagents used in master mix + water

get_mm_dicts

get_mm_dicts(mm_df: pd.DataFrame, reagents_df: pd.DataFrame) -> Tuple[Dict[str, List[Tuple[str, str, str]]], Dict]

Master mix dictionary purely for use in the assembly script. Provides instructions on tranfers.

Arguments:

mm_df = dataframe of master mix, gives wells and diff vol needed reagents_df = dataframe of reagents to be used in master mix and other parts of assembly

Returns:

  • reagent_to_mm_dict - dictionary directing where to transfer each reagent to to make master mixes, key = reagent well, value = list of tuples of reagent plate (different for water and other reagents), master mix well, and volume to be transferred mm_dict_list = mm_df rows stored as dictionaries in list

index_to_well_name

index_to_well_name(no: int) -> str

Converts well from number format to letter format Args: well in number format e.g. 0 Returns: well in letter format e.g. 'A1'

create_transform_metainformation

create_transform_metainformation(output_path: str, labware_dict: Dict[str, str], triplicate: str, multi: bool)

Saves transform metainformation and labware informaiton. SOC used in two steps: adding soc (150 uL) and dilution (45 uL) times by 96 as reaction plate has 96 wells Add 300 (1502) and 90 (452) as dead vols Agar plate positions in agar plate csv

Arguments:

  • output_path - absolute path to transformation metainformation file
  • labware_dict - dictionary of labware to be used
  • triplicate - whether 'single' (triplicate = False) or 'triplicate' (triplicate = True) is selected
  • multi - whether an 8 channel (multi = True) or single channel (mutli = False) p300 pipette is being used

create_protocol

create_protocol(dna_plate_map_dict: Dict[str, List], combinations_to_make: List[Dict], reagent_to_mm_dict: Dict, mm_dict: Dict, assembly_template_path: str, transform_template_path: str, output_folder_path: str, thermocycle: bool, triplicate: str, multi: bool, p10Mount: str, p300Mount: str, p10_type: str, p300_type: str, reaction_plate_type: str, reagent_plate_type: str, trough_type: str, agar_plate_type: str) -> Tuple[str, str]

Generates the assembly and transformation protocols used by opentrons. Returns the paths of the assembly and transform scripts.

Arguments:

  • dna_plate_map_dict - the dictionary of parts
  • combinations_to_make - the list of dictionaries of constructs
  • reagent_to_mm_dict - dictionary directing where to transfer each reagent to to make master mixes, key = reagent well, value = list of tuples of reagent plate (different for water and other reagents), master mix well, and volume to be transferred mm_dict_list = mm_df rows stored as dictionaries in list
  • assembly_template_path - the absolute path of the assembly template script
  • transform_template_path - the absolute path of the transformation template script
  • output_folder_path - the absolute path to the output folder that will contain the assembly and transformation protocols
  • thermocycle - whether or not the Opentrons thermocycler module is being used
  • triplicate - whether 'single' (triplicate = False) or 'triplicate' (triplicate = True) is selected
  • multi - whether an 8 channel (multi = True) or single channel (mutli = False) p300 pipette is being used
  • p10_mount - "left" or "right", the Opentrons pipette mount options
  • p300_mount - "left" or "right", the Opentrons pipette mount options
  • p10_type - the name of the p10 pipette, e.g. "p10_single"
  • p300_type - the name of the p300 pipette, e.g. "p300_single"
  • reaction_plate_type - the name of the well plate type used as the source and construct plate
  • reagent_plate_type - the name of the well plate type used as the reagent plate (for master mix and non-water reagents)
  • trough_type - the name of the trough type used for water and soc
  • agar_plate_type - the name of the agar plate type used
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