comparison CreateAssemblyPicklists_script.py @ 1:196e13c09881 draft

planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit fe52aec22c97cd357d1b6c40c2954d27ebad87d3-dirty

0:4bde3e90ee98

        new_path = path.replace("__sq__", "'")
        if new_path != path:
            os.rename(path, new_path)
        fixed_paths.append(new_path)
    return fixed_paths


def did_you_mean(name, other_names, limit=5, min_score=50):  # test
    results = process.extract(name, list(other_names), limit=limit)
    return [e for (e, score) in results if score >= min_score]

    parser = argparse.ArgumentParser(description="Generate picklist for DNA assembly.")
    parser.add_argument("--parts_files", help="Directory with parts data or file with part sizes")
    parser.add_argument("--picklist", type=str, help="Path to the assembly plan CSV or Excel file")
    parser.add_argument("--source_plate", help="Source plate file (CSV or Excel)")
    parser.add_argument("--backbone_name", help="Name of the backbone")
    parser.add_argument("--result_zip", help="Name of the output zip file")
    parser.add_argument("--part_backbone_ratio", type=float, help="Part to backbone molar ratio")
    parser.add_argument("--quantity_unit", choices=["fmol", "nM", "ng"], help="Quantity unit")
    parser.add_argument("--part_quantity", type=float, help="Quantity of each part")
    parser.add_argument("--buffer_volume", type=float, help="Buffer volume in µL")
    parser.add_argument("--total_volume", type=float, help="Total reaction volume in µL")
    parser.add_argument("--dispenser", choices=["labcyte_echo", "tecan_evo"], help="Dispenser machine")

        complement_to=total_volume * 1e-6,  # convert uL to L
        buffer_volume=buffer_volume * 1e-6,
        volume_rounding=2.5e-9,  # not using parameter from form
        minimal_dispense_volume=5e-9,  # Echo machine's minimum dispense -
    )
    backbone_name_list = backbone_name.split(",")
    source_plate = plate_from_content_spreadsheet(source_plate_path)

    for well in source_plate.iter_wells():
        if well.is_empty:
            continue
        quantities = well.content.quantities
        part, quantity = list(quantities.items())[0]
        quantities.pop(part)
        quantities[part.replace(" ", "_")] = quantity

        if part in backbone_name_list:
            # This section multiplies the backbone concentration with the
            # part:backbone molar ratio. This tricks the calculator into making
            # a picklist with the desired ratio.
            # For example, a part:backbone = 2:1 will multiply the
            # backbone concentration by 2, therefore half as much of it will be
            # added to the well.
            quantities[part.replace(" ", "_")] = quantity * part_backbone_ratio
        else:
            quantities[part.replace(" ", "_")] = quantity

    source_plate.name = "Source"
    if destination_plate:
        dest_filelike = file_to_filelike_object(destination_plate)
        destination_plate = plate_from_content_spreadsheet(destination_plate)

1:196e13c09881

        new_path = path.replace("__sq__", "'")
        if new_path != path:
            os.rename(path, new_path)
        fixed_paths.append(new_path)
    return fixed_paths


def parse_optional_float(x):
    if x == '':
        return None
    return float(x)


def did_you_mean(name, other_names, limit=5, min_score=50):  # test
    results = process.extract(name, list(other_names), limit=limit)
    return [e for (e, score) in results if score >= min_score]

    parser = argparse.ArgumentParser(description="Generate picklist for DNA assembly.")
    parser.add_argument("--parts_files", help="Directory with parts data or file with part sizes")
    parser.add_argument("--picklist", type=str, help="Path to the assembly plan CSV or Excel file")
    parser.add_argument("--source_plate", help="Source plate file (CSV or Excel)")
    parser.add_argument("--backbone_name", required=False, help="Name of the backbone")
    parser.add_argument("--result_zip", help="Name of the output zip file")
    parser.add_argument("--part_backbone_ratio", type=parse_optional_float, required=False, help="Part to backbone molar ratio")
    parser.add_argument("--quantity_unit", choices=["fmol", "nM", "ng"], help="Quantity unit")
    parser.add_argument("--part_quantity", type=float, help="Quantity of each part")
    parser.add_argument("--buffer_volume", type=float, help="Buffer volume in µL")
    parser.add_argument("--total_volume", type=float, help="Total reaction volume in µL")
    parser.add_argument("--dispenser", choices=["labcyte_echo", "tecan_evo"], help="Dispenser machine")

        complement_to=total_volume * 1e-6,  # convert uL to L
        buffer_volume=buffer_volume * 1e-6,
        volume_rounding=2.5e-9,  # not using parameter from form
        minimal_dispense_volume=5e-9,  # Echo machine's minimum dispense -
    )
    if backbone_name != '' and backbone_name != 'Non':
        backbone_name_list = backbone_name.split(",")
    source_plate = plate_from_content_spreadsheet(source_plate_path)

    for well in source_plate.iter_wells():
        if well.is_empty:
            continue
        quantities = well.content.quantities
        part, quantity = list(quantities.items())[0]
        quantities.pop(part)
        quantities[part.replace(" ", "_")] = quantity

        if backbone_name != '' and backbone_name != 'Non':
            if part in backbone_name_list:
                # This section multiplies the backbone concentration with the
                # part:backbone molar ratio. This tricks the calculator into making
                # a picklist with the desired ratio.
                # For example, a part:backbone = 2:1 will multiply the
                # backbone concentration by 2, therefore half as much of it will be
                # added to the well.
                quantities[part.replace(" ", "_")] = quantity * part_backbone_ratio
            else:
                quantities[part.replace(" ", "_")] = quantity

    source_plate.name = "Source"
    if destination_plate:
        dest_filelike = file_to_filelike_object(destination_plate)
        destination_plate = plate_from_content_spreadsheet(destination_plate)