Lab Helpers

Convenience functions to help direct large-scale slat assembly and purification are also available.

crisscross.helper_functions.lab_helper_sheet_generation ¶

next_excel_column_name ¶

next_excel_column_name(n)

Given a 0-based index, return the Excel-style column name.

apply_box_border ¶

apply_box_border(ws, top_left, top_right, bottom_left, bottom_right, style='thick')

Applies a thick border to an excel sheet surrounding the specified cells.

PARAMETER	DESCRIPTION
`ws`	Excel worsheet object.
`top_left`	Top left cell.
`top_right`	Top right cell.
`bottom_left`	Bottom left cell.
`bottom_right`	Bottom right cell.
`style`	Border style to be applied. DEFAULT: `'thick'`

RETURNS	DESCRIPTION
	N/A, applied in-place.

adjust_column_width ¶

adjust_column_width(ws)

Adjusts the column width of an excel sheet based on the maximum length of the content in each column.

PARAMETER	DESCRIPTION
`ws`	Excel sheet object.

RETURNS	DESCRIPTION
	N/A, adjusted in-place.

prepare_master_mix_sheet ¶

prepare_master_mix_sheet(
    slat_dict,
    echo_sheet=None,
    reference_handle_volume=150,
    reference_handle_concentration=500,
    slat_mixture_volume=50,
    unique_transfer_volume_plates=None,
    workbook=None,
    handle_mix_ratio=10,
    split_core_staple_pools=False,
)

Prepares a 'master mix' sheet to be used for combining slat mixtures with scaffold and core staples into the final slat mixture.

PARAMETER	DESCRIPTION
`slat_dict`	Dictionary of slats with slat names as keys and slat objects as values.
`echo_sheet`	Exact list of commands sent to the Echo robot for this group of slats. DEFAULT: `None`
`reference_handle_volume`	Reference staple volume for each handle in a pool in nL (this refers to the control handles plate). DEFAULT: `150`
`reference_handle_concentration`	Reference staple concentration used for the core staples in uM (this refers to the control handles plate). All concentration values will be referenced to this value. DEFAULT: `500`
`slat_mixture_volume`	Reaction volume (in uL) for a single slat annealing mixture. Can be set to 'max' to use up all available handle mix. DEFAULT: `50`
`handle_mix_ratio`	Ratio of handle mix concentration to scaffold concentration (default is 10). DEFAULT: `10`
`unique_transfer_volume_plates`	Plates that have special non-standard volumes. This will be ignored if the echo sheet is provided with the exact details. DEFAULT: `None`
`workbook`	The workbook to which the new excel sheet should be added. DEFAULT: `None`
`split_core_staple_pools`	If True, the core staples will be assumed to have been split into 4 pools (S0, S1, S3, S4). DEFAULT: `False`

RETURNS	DESCRIPTION
	Workbook with new sheet included.

prepare_peg_purification_sheet ¶

prepare_peg_purification_sheet(
    slat_dict,
    groups_per_layer=2,
    max_slat_concentration_uM=2,
    slat_mixture_volume=50,
    workbook=None,
    echo_sheet=None,
    special_slat_groups=None,
    peg_concentration=2,
)

Prepares standard instructions for combining and purifying slat mixtures using PEG purification. Also prepares lists of slat groups as a reference for when in the lab.

PARAMETER	DESCRIPTION
`slat_dict`	Dictionary of slats with slat names as keys and slat objects as values.
`groups_per_layer`	Number of PEG groups to use per crisscross layer. You might want to adjust this if you have too many slats together in one group. DEFAULT: `2`
`max_slat_concentration_uM`	Maximum concentration of slats in a combined PEG mixture (in UM) before a warning is triggered. DEFAULT: `2`
`slat_mixture_volume`	Reaction volume (in uL) for a single slat annealing mixture. DEFAULT: `50`
`workbook`	The workbook to which the new excel sheet should be added. DEFAULT: `None`
`echo_sheet`	Exact list of commands sent to the Echo robot for this group of slats. DEFAULT: `None`
`special_slat_groups`	IDs of slats that should be separated from the general slat groups and placed in their own group. DEFAULT: `None`
`peg_concentration`	PEG concentration (in terms of X) to be used as the stock solution for the purification step. DEFAULT: `2`

RETURNS	DESCRIPTION
	Workbook with new sheet included.

prepare_all_standard_sheets ¶

prepare_all_standard_sheets(
    slat_dict,
    save_filepath,
    reference_single_handle_volume=150,
    reference_single_handle_concentration=500,
    slat_mixture_volume=50,
    peg_groups_per_layer=2,
    peg_concentration=2,
    echo_sheet=None,
    max_slat_concentration_uM=2,
    unique_transfer_volume_plates=None,
    special_slat_groups=None,
    handle_mix_ratio=10,
    split_core_staple_pools=False,
)

Prepares a series of excel sheets to aid lab assembler while preparing and purifying slat mixtures.

PARAMETER	DESCRIPTION
`slat_dict`	Dictionary of slats to be assembled (each item in the dict is a Slat Object containing all 64 handles in place)
`save_filepath`	Output file path for the combined excel workbook
`reference_single_handle_volume`	Reference staple volume for each handle in a pool in nL (this refers to the control handles plate). DEFAULT: `150`
`reference_single_handle_concentration`	Reference staple concentration used for the core staples in uM (this refers to the control handles plate). All concentration values will be referenced to this value. DEFAULT: `500`
`slat_mixture_volume`	Reaction volume (in uL) for a single slat annealing mixture. Can be set to 'max' to use up all available handle mix. DEFAULT: `50`
`peg_groups_per_layer`	Number of PEG groups to use per crisscross layer. You might want to adjust this if you have too many slats together in one group. DEFAULT: `2`
`peg_concentration`	PEG concentration (in terms of X) to be used as the stock solution for the purification step. DEFAULT: `2`
`echo_sheet`	Exact echo commands to use as a reference for calculating slat concentrations. DEFAULT: `None`
`max_slat_concentration_uM`	Maximum concentration of slats in a combined PEG mixture (in UM) before a warning is triggered. DEFAULT: `2`
`unique_transfer_volume_plates`	Plates that have special non-standard volumes. This will be ignored if the echo sheet is provided with the exact details. DEFAULT: `None`
`special_slat_groups`	IDs of slats that should be separated from the general slat groups and placed in their own group. DEFAULT: `None`
`handle_mix_ratio`	Ratio of handle mix concentration to scaffold concentration (default is 10). DEFAULT: `10`
`split_core_staple_pools`	If True, the core staples will be assumed to have been split into 4 pools (S0, S1, S3, S4). DEFAULT: `False`

RETURNS	DESCRIPTION
	N/A, file saved directly to disk.

prepare_liquid_handle_plates_multiple_files ¶

prepare_liquid_handle_plates_multiple_files(
    output_directory,
    file_list=None,
    extract_all_from_folder=None,
    target_concentration_uM=1000,
    volume_cap_ul=120,
    target_concentration_per_plate=None,
    max_commands_per_file=None,
    plot_distribution_per_plate=True,
    plate_size="384",
)

Generates resuspension maps for all provided DNA spec files.

PARAMETER	DESCRIPTION
`output_directory`	Output folder to save noflank_results.
`file_list`	Specific list of filepaths to assess. DEFAULT: `None`
`extract_all_from_folder`	Alternatively, specify a folder and all excel sheets will be extracted from the folder. DEFAULT: `None`
`target_concentration_uM`	Target concentration for plate resuspension. DEFAULT: `1000`
`volume_cap_ul`	Maximum volume to resuspend (after which the volume is kept constant and the concentration is raised instead). DEFAULT: `120`
`target_concentration_per_plate`	Set to a dictionary of concentrations per plate if different concentrations are desired for different plates. DEFAULT: `None`
`max_commands_per_file`	Maximum commands that can be taken in by the liquid handler in one go. If this is exceeded, files are split into different components. DEFAULT: `None`
`plot_distribution_per_plate`	If true, generate a volume distribution plot for each plate. DEFAULT: `True`
`plate_size`	Specify the size of the plate to generate. DEFAULT: `'384'`

RETURNS	DESCRIPTION
	N/A

prepare_liquid_handler_plate_resuspension_map ¶

prepare_liquid_handler_plate_resuspension_map(
    filename,
    output_directory,
    target_concentration_uM=1000,
    volume_cap_ul=120,
    max_commands_per_file=None,
    plot_distribution_per_plate=True,
    target_concentration_per_plate=None,
    plate_size="384",
)

Generates a visual plate map and resuspension instructions for an entire plate of DNA oligos. The amount of DNA per well should be specified in an excel file using the standard IDT format.

PARAMETER	DESCRIPTION
`filename`	Excel file containing DNA spec sheets (can contain multiples plates per sheet).
`output_directory`	Output folder to save noflank_results.
`target_concentration_uM`	Target concentration for plate resuspension. DEFAULT: `1000`
`volume_cap_ul`	Maximum volume to resuspend (after which the volume is kept constant and the concentration is raised instead). DEFAULT: `120`
`max_commands_per_file`	Maximum commands that can be taken in by the liquid handler in one go. If this is exceeded, files are split into different components. DEFAULT: `None`
`plot_distribution_per_plate`	If true, generate a volume distribution plot for each plate. DEFAULT: `True`
`target_concentration_per_plate`	Set to a dictionary of concentrations per plate if different concentrations are desired for different plates. DEFAULT: `None`
`plate_size`	Specify the size of the plate to generate. DEFAULT: `'384'`

RETURNS	DESCRIPTION
	Distribution of volumes generated from the specified file.

visualize_plate_volume_distribution ¶

visualize_plate_volume_distribution(file_output, volume_dist, target_concentration_uM)

Visualizes the distribution of resuspension volumes for a given list.

PARAMETER	DESCRIPTION
`file_output`	Output filename
`volume_dist`	List of volumes (in ul)
`target_concentration_uM`	Target concentration used for this particular plate

RETURNS	DESCRIPTION
	N/A