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Plater

This module is for generating a Tecan EVO gwl picklist file from a csv file that specifies the transfers. See data.csv for the required data and columns.

Install

The package is not available on PyPI. Install from Github:

pip install plater@git+https://github.com/Edinburgh-Genome-Foundry/Plater

Usage:

import plater
import plateo

Optional: load destination plate

destination_plate = plateo.parsers.plate_from_content_spreadsheet("example_echo_plate.xlsx")

Generate gwl from csv specifications:

gwl_and_platemap = plater.create_gwl_and_platemap_from_csv(name="test",
                                                           csv_file="data.csv",
                                                           starting_well=1,  # default
                                                           washing_scheme=None,  # default
                                                           destination_plate=destination_plate)
# The default destination_plate=None generates a plate according to the csv file.

gwl_and_platemap.keys()
# dict_keys(['gwl',     # dioscuri.GeminiWorkList()
#            'plate',   # plateo.Plate()
#            'report']) # string of comments
# GeminiWorkList:
gwl_and_platemap["gwl"].records_to_file("picklist.gwl")
# Destination Plate:
plateo.exporters.plate_to_content_spreadsheet(gwl_and_platemap["plate"],
                                              "dest_plate_for_data_csv.xlsx")
# Report on run:
print(gwl_and_platemap["report"])

Generate gwl from Geneart shipment sheet (edit then use with function above):

geneart_plate_csv = plater.convert_geneart_shipment_file_to_csv(
                                            filepath="geneart_example.xlsx",
                                            destination_plate_name="Destination",
                                            destination_plate_type="Echo PP P-05525 raised",
                                            destination_plate_size=384,
                                            destination_csv="geneart_example_transfer.csv")
# Optional: edit df, then:
geneart_plate_csv.to_csv("transfer.csv", index=False)

Generate plate from Geneart shipment sheet (updated version of Plateo's function):

geneart_plates = plater.plates_from_geneart_shipment_layout_sheet("geneart_example.xlsx")

This returns a list of plates that can be exported into content spreadsheets as shown above.

Transfer clones specified by the CUBA Analyze Digests app:

plate_data = plater.make_csv_from_fragment_analyzer_report(filepath="fragment_analyzer.csv",
                                              destination_plate_name="Destination",
                                              destination_plate_type="4ti-0960/B raised",
                                              destination_plate_size=96,
                                              volume_to_transfer=40,
                                              destination_csv="fragment_analyzer_transfer.csv",
                                              source_plate_name="Source1",
                                              source_plate_type="4ti-0960/B on CPAC",
                                              source_plate_size=96,
                                             )
fa_gwl_and_platemap = plater.create_gwl_and_platemap_from_csv(name="FA_test",
                                                              csv_file="fragment_analyzer_transfer.csv",
                                                              starting_well=1,  # default
                                                              washing_scheme=None  # default
                                                             )
fa_gwl_and_platemap["gwl"].records_to_file("fragment_analyzer_transfer.gwl")

License = MIT

Plater is free software, which means the users have the freedom to run, copy, distribute, study, change and improve the software.

Plater was written at the Edinburgh Genome Foundry by Peter Vegh and is released under the MIT license.