Helper Functions

Slat Design¶

Basic tools for designing DNA slats.

crisscross.core_functions.slat_design ¶

generate_standard_square_slats ¶

generate_standard_square_slats(slat_count=32)

Generates a base array for a square megastructure design

PARAMETER	DESCRIPTION
`slat_count`	Number of handle positions in each slat DEFAULT: `32`

RETURNS	DESCRIPTION
	3D numpy array with x/y slat positions and a list of the unique slat IDs for each layer

read_design_from_excel ¶

read_design_from_excel(folder, sheets)

Reads a megastructure design pre-populated in excel. 0s indicate no slats, all other numbers are slat IDs

PARAMETER	DESCRIPTION
`folder`	Folder containing excel sheets
`sheets`	List of sheets containing the positions of slats (in order, starting from the bottom layer)

RETURNS	DESCRIPTION
	3D numpy array with x/y slat positions

attach_cargo_handles_to_core_sequences ¶

attach_cargo_handles_to_core_sequences(
    pattern, sequence_map, target_plate, slat_type="X", handle_side=2
)

TODO: extend for any shape (currently only 2D squares) Concatenates cargo handles to provided sequences according to cargo pattern.

PARAMETER	DESCRIPTION
`pattern`	2D array showing where each cargo handle will be attached to a slat
`sequence_map`	Sequence to use for each particular cargo handle in pattern
`target_plate`	Plate class containing all the pre-mapped sequences/wells for the selected slats
`slat_type`	Type of slat to attach to (X or Y) DEFAULT: `'X'`
`handle_side`	H2 or H5 handle position DEFAULT: `2`

RETURNS	DESCRIPTION
	Dataframe containing all new sequences to be ordered for cargo attachment

generate_patterned_square_cco ¶

generate_patterned_square_cco(pattern='2_slat_jump')

Pre-generates a square megastructure with specific repeating patterns.

PARAMETER	DESCRIPTION
`pattern`	Choose from the set of available pre-made patterns. DEFAULT: `'2_slat_jump'`

RETURNS	DESCRIPTION
	2D array containing pattern TODO: make size of square adjustable

General Helper Functions¶

General utility functions.

crisscross.helper_functions ¶

revcom ¶

revcom(sequence)

Reverse complements a DNA sequence.

PARAMETER	DESCRIPTION
`sequence`	DNA string, do not add any other characters (TODO: make more robust)

RETURNS	DESCRIPTION
	processed sequence (string)

create_dir_if_empty ¶

create_dir_if_empty(*directories)

Creates a directory if it doesn't exist.

PARAMETER	DESCRIPTION
`directories`	Single filepath or list of filepaths. DEFAULT: `()`

RETURNS	DESCRIPTION
	N/A

clear_folder_contents ¶

clear_folder_contents(root_folder)

Deletes all files in selected folder.

PARAMETER	DESCRIPTION
`root_folder`	Folder within which all files should be deleted.

RETURNS	DESCRIPTION
	N/A

zip_folder_to_disk ¶

zip_folder_to_disk(folder_path, output_zip_path)

Zips a folder into a zip file.

PARAMETER	DESCRIPTION
`folder_path`	Location of the folder to be zipped.
`output_zip_path`	New zip file location.

RETURNS	DESCRIPTION
	N/A

index_converter ¶

index_converter(ind, images_per_row, double_indexing=True)

Converts a singe digit index into a double digit system, if required.

PARAMETER	DESCRIPTION
`ind`	The input single index
`images_per_row`	The number of images per row in the output figure
`double_indexing`	Whether or not double indexing is required DEFAULT: `True`

RETURNS	DESCRIPTION
	Two split indices or a single index if double indexing not necessary

save_list_dict_to_file ¶

save_list_dict_to_file(
    output_folder,
    filename,
    lists_dict,
    selected_data=None,
    append=True,
    index_column=None,
)

Saves a dictionary of lists to an excel file.

PARAMETER	DESCRIPTION
`output_folder`	Folder to save final file
`filename`	Name of the file to save
`lists_dict`	Dictionary of lists. Each key will become a column header, while the data will be saved in rows. Each list must have the same length.
`selected_data`	Optional list of specific indices to save. If None, all data will be saved. DEFAULT: `None`
`append`	Set to true to append to an existing file if this is available. DEFAULT: `True`
`index_column`	Optional column name to move to the left-most position in the output file. DEFAULT: `None`

RETURNS	DESCRIPTION
	N/A

convert_np_to_py ¶

convert_np_to_py(data)

Converts numpy data types to python data types. Only works on integers, floats and ndarrays.

PARAMETER	DESCRIPTION
`data`	Numpy data, dictionary of numpy data or list of numpy data

RETURNS	DESCRIPTION
	Updated data