Plate Handling

Functions for managing laboratory plates and protocols.

Main plate reader class¶

crisscross.plate_mapping.hash_cad_plates ¶

HashCadPlate ¶

HashCadPlate(
    plate_name,
    plate_folder,
    pre_read_plate_dfs=None,
    plate_size=384,
    apply_working_stock_concentration=None,
)

A standardized plate system that defines the same ID pattern for all possible handle types (cargo, assembly, seed, etc.). This same system can be read into #-CAD directly. Each plate also features a 2D layout tab to help visualize in the lab.

identify_wells_and_sequences ¶

identify_wells_and_sequences()

Identifies wells and sequences from the plate data and combines them into one database.

get_sequence ¶

get_sequence(category, slat_position, slat_side, cargo_id=0)

To retrieve data from the database, the following keys are required: - category: 'cargo', 'assembly', 'seed', etc. - slat_position: physical slat handle ID i.e. 1, 2, ..., 32 - slat_side: i.e. 2, 5 (for h2/h5 handles) - cargo_id: e.g., 'A', 'B', ..., 'Z' (for cargo plates) or 1-64 for assembly handles

get_well ¶

get_well(category, slat_position, slat_side, cargo_id=0)

To retrieve data from the database, the following keys are required: - category: 'cargo', 'assembly', 'seed', etc. - slat_position: physical slat handle ID i.e. 1, 2, ..., 32 - slat_side: i.e. 2, 5 (for h2/h5 handles) - cargo_id: e.g., 'A', 'B', ..., 'Z' (for cargo plates) or 1-64 for assembly handles

get_concentration ¶

get_concentration(category, slat_position, slat_side, cargo_id=0)

To retrieve data from the database, the following keys are required: - category: 'cargo', 'assembly', 'seed', etc. - slat_position: physical slat handle ID i.e. 1, 2, ..., 32 - slat_side: i.e. 2, 5 (for h2/h5 handles) - cargo_id: e.g., 'A', 'B', ..., 'Z' (for cargo plates) or 1-64 for assembly handles

get_plate_name ¶

get_plate_name(category, slat_position, slat_side, cargo_id)

To retrieve data from the database, the following keys are required: - category: 'cargo', 'assembly', 'seed', etc. - slat_position: physical slat handle ID i.e. 1, 2, ..., 32 - slat_side: i.e. 2, 5 (for h2/h5 handles) - cargo_id: e.g., 'A', 'B', ..., 'Z' (for cargo plates) or 1-64 for assembly handles

Utility functions¶

crisscross.plate_mapping ¶

get_plateclass ¶

get_plateclass(name, plate_name, plate_folder, **kwargs)

Main model extractor.

PARAMETER	DESCRIPTION
`name`	Plate class name.
`plate_name`	Name/s of selected plate file/s.
`plate_folder`	Plate folder location

RETURNS	DESCRIPTION
	instantiated plate reader class.

get_assembly_handle_v2_sample_plates ¶

get_assembly_handle_v2_sample_plates()

Generates plates used for the initial testing of assembly handle library v2.

get_standard_plates ¶

get_standard_plates(handle_library_v2=False)

Generates standard plates used commonly in most designs.

get_cutting_edge_plates ¶

get_cutting_edge_plates(handle_library_working_stock_concentration=None)

Generates standard plates used commonly in most designs. These are the most updated plates in the current library.

get_cargo_plates ¶

get_cargo_plates()

Generates standard cargo plates used commonly in most designs.

Standard plate names (change for your system if necessary)¶

crisscross.plate_mapping.plate_constants ¶

sanitize_plate_map ¶

sanitize_plate_map(name)

Actual plate name for the Echo always just features the person's name and the plate ID.

PARAMETER	DESCRIPTION
`name`	Long-form plate name

RETURNS	DESCRIPTION
	Barebones plate name for Echo

Methods for generating and editing plates¶

crisscross.core_functions.plate_handling ¶

add_data_to_plate_df ¶

add_data_to_plate_df(letters, column_total, data_dict)

Creates an empty plate (i.e. with rows/columns premade) and inserts provided data dict, leaving all empty cells blank.

PARAMETER	DESCRIPTION
`letters`	Letters to use for rows.
`column_total`	Total amount of columns (numbers)
`data_dict`	Nested dictionary containing data to input into plate (keys are letters, values are dictionaries with numbers as keys)

RETURNS	DESCRIPTION
	Updated plate

read_dna_plate_mapping ¶

read_dna_plate_mapping(filename, data_type='2d_excel', plate_size=384)

Reads a DNA plate mapping file and returns a dataframe with the data.

PARAMETER	DESCRIPTION
`filename`	Filename to read (full path)
`data_type`	Type of data - currently only supports 2d_excel and IDT_order DEFAULT: `'2d_excel'`
`plate_size`	Either 96 or 384-well plate sizes DEFAULT: `384`

RETURNS	DESCRIPTION
	Dataframe containing all data

generate_new_plate_from_slat_handle_df ¶

generate_new_plate_from_slat_handle_df(
    data_df,
    folder,
    filename,
    restart_row_by_column=None,
    data_type="2d_excel",
    plate_size=384,
    plate_name=None,
    scramble_names=False,
    output_generic_cargo_plate_mapping=False,
)

Generates a new plate from a dataframe containing sequences, names and notes, then saves it to file. TODO: make faster and more elegant.

PARAMETER	DESCRIPTION
`data_df`	Main sequence data to export containing sequence, name and description.
`folder`	Output folder.
`filename`	Output filename.
`restart_row_by_column`	Set this to a column name to restart the row number when the value changes. DEFAULT: `None`
`data_type`	Either 2d_excel (2d output array) or IDT_order (for IDT order form). DEFAULT: `'2d_excel'`
`plate_size`	96 or 384 DEFAULT: `384`
`plate_name`	Name of the plate (used for IDT order form) DEFAULT: `None`
`scramble_names`	If true, scrubs all identifiable names when preparing an IDT order output DEFAULT: `False`
`output_generic_cargo_plate_mapping`	If true, outputs the generic cargo plate mapping naming schemes to the 'names' sheet so that the generic cargo plate system can be used directly from the generated file DEFAULT: `False`

RETURNS	DESCRIPTION
	final dataframe that's saved to file

Method for visualizing a plate's contents¶

crisscross.helper_functions.simple_plate_visuals ¶

visualize_plate_with_color_labels ¶

visualize_plate_with_color_labels(
    plate_size,
    well_color_dict,
    color_label_dict=None,
    well_label_dict=None,
    plate_title=None,
    save_folder=None,
    save_file=None,
    direct_show=True,
    plate_display_aspect_ratio=1.495,
)

Use this function to create a plate graphic with specific colours placed in each well, and alternatively a unique label for each well too.

PARAMETER	DESCRIPTION
`plate_size`	'384' or '96'
`well_color_dict`	Dictionary containing colour to be placed in specific wells.
`color_label_dict`	Legend to use for specific colours (at the bottom of the image) DEFAULT: `None`
`well_label_dict`	Optional label to place in specific wells DEFAULT: `None`
`plate_title`	Title to display above plate DEFAULT: `None`
`save_folder`	Output folder DEFAULT: `None`
`save_file`	Output file name DEFAULT: `None`
`direct_show`	Set to true to display the image directly DEFAULT: `True`
`plate_display_aspect_ratio`	Aspect ratio to use for plate display DEFAULT: `1.495`

RETURNS	DESCRIPTION
	N/A