def reset(self): TxtWriter.reset(self) self.__support_mastermix = None self.__library = None self.__parameter_values = None self.__iso_conc = None self.__final_conc = None
def __init__(self, donor_racks, receiver_racks, excluded_racks, racks_to_empty, parent=None): """ Constructor. :param dict donor_racks: The donor racks mapped onto rack barcodes. :param dict receiver_racks: The receiver racks mapped onto rack barcodes. :param list excluded_racks: Barcodes from racks that should not be used. :param int racks_to_empty: The number of empty racks the run shall result in. """ TxtWriter.__init__(self, parent=parent) #: The donor racks mapped onto rack barcodes. self.donor_racks = donor_racks #: The receiver racks mapped onto rack barcodes. self.receiver_racks = receiver_racks #: Barcodes from racks that shall not be used. self.excluded_racks = excluded_racks #: The number of empty racks the run shall result in (optional). self.racks_to_empty = racks_to_empty
def __init__(self, iso, tube_transfers, source_rack_locations, sector_index=None, has_pool_stock_racks=True, parent=None): """ Constructor. :param iso: The library creation ISO for which to generate the file. :type iso: :class:`thelma.entities.iso.StockSampleCreationIso` :param tube_transfers: Define which tube goes where. :type tube_transfers: :class:`TubeTransfer`# :param int sector_index: Sector of the rack being created. If this is not given, no sector information will be included in the header. :param dict source_rack_locations: Map rack barcode -> rack location. :param bool has_pool_stock_racks: Flag indicating if the ISO being processed will create stock pool racks. """ TxtWriter.__init__(self, parent=None) self.tube_transfers = tube_transfers self.iso = iso self.source_rack_locations = source_rack_locations self.sector_index = sector_index self.has_pool_stock_racks = has_pool_stock_racks
def __init__(self, tube_transfers, library_name, layout_number, sector_index, source_rack_locations, parent=None): """ Constructor. :param tube_transfers: Define which tube goes where. :type tube_transfers: :class:`TubeTransfer`# :param str library_name: The library we are creating. :param int layout_number: the layout for which we are creating racks :param int sector_index: The sector we are dealing with. :param source_rack_locations: Maps rack locations onto rack barcodes. :type source_rack_locations: :class:`dict` """ TxtWriter.__init__(self, parent=None) #: Define which tube goes where. self.tube_transfers = tube_transfers #: The library we are creating. self.library_name = library_name #: The layout for which we are creating racks self.layout_number = layout_number #: The sector we are dealing with. self.sector_index = sector_index #: Maps rack locations onto rack barcodes. self.source_rack_locations = source_rack_locations
def __init__(self, library_creation_iso, pool_stock_racks, tube_destination_racks, parent=None): """ Constructor. :param library_creation_iso: The library creation ISO for which to generate the file. :type library_creation_iso: :class:`thelma.entities.library.LibraryCreationIso` :param tube_destination_racks: The barcodes for the destination rack for the single molecule design tube (these racks have to be empty). :type tube_destination_racks: map of barcode lists (:class:`basestring`) mapped onto sector indices. :param pool_stock_racks: The barcodes for the pool stock racks (these racks have to have empty tubes in defined positions). :type pool_stock_racks: map of barcodes (:class:`basestring`) mapped onto sector indices. """ TxtWriter.__init__(self, parent=parent) #: The library creation ISO for which to generate the file. self.library_creation_iso = library_creation_iso #: The barcodes for the destination, rack for the single molecule #: design tubes. self.tube_destination_racks = tube_destination_racks #: The barcodes for the pool stock racks. self.pool_stock_racks = pool_stock_racks #: The library source (preparation) plates mapped onto #: rack sectors. self.__source_plates = None
def __init__(self, generator, number_replicates, supports_mastermix, reservoir_specs, parent=None): """ Constructor. :param generator: The experiment metadata generator. :type generator: :class:`ExperimentMetadataGenerator` :param int number_replicates: The number of replicates planned for this experiment design (positive number). :param bool supports_mastermix: Indicates if the values support mastermix preparation. :param reservoir_specs: The reservoir specs of the ISO plate. :type reservoir_specs: :class:`thelma.entities.liquidtransfer.ReservoirSpecs` """ TxtWriter.__init__(self, parent=parent) #: The experiment metadata generator. self.generator = generator #: The planned number of replicates. self.number_replicates = number_replicates #: Do the values support mastermix preparation? self.supports_mastermix = supports_mastermix #: The reservoir specs of the ISO plate. self.reservoir_specs = reservoir_specs
def __init__(self, rack_barcodes, tube_transfers, parent=None): """ Constructor. :param list rack_barcodes: A list of the racks that have been scanned. :param list tube_transfers: The tube transfers scheduled by the RackScanningAdjuster (:class:`TubeTransferData` objects). """ TxtWriter.__init__(self, parent=parent) #: The racks that have been scanned. self.rack_barcodes = rack_barcodes #: The scheduled tube transfers. self.tube_transfers = tube_transfers
def __init__(self, generator, em_label, parent=None): """ Constructor. :param generator: The experiment metadata generator. :type generator: :class:`ExperimentMetadataGenerator` :param str em_label: The label of the experiment metadata. """ TxtWriter.__init__(self, parent=parent) #: The experiment metadata generator. self.generator = generator #: The label of the experiment metadata. self.em_label = em_label
def __init__(self, xl20_worklist_stream, **kw): """ Constructor: :param xl20_worklist_stream: An XL20 worklist containing the robot instructions as stream (e.g. created by the :class:`XL20WorklistWriter`). :type xl20_worklist_stream: stream (CSV) """ TxtWriter.__init__(self, **kw) #: The XL20 worklist containing the robot instructions as stream. self.xl20_worklist_stream = xl20_worklist_stream #: The tube transfers parsed from the input file as #: :class:`TubeTransferData` objects. self.tube_transfers = None
def __init__(self, generator, parent=None): """ Constructor. :param generator: The experiment metadata generator used for the upload. :type generator: :class:`ExperimentMetadataGeneratorLibrary` """ TxtWriter.__init__(self, parent=parent) #: The experiment metadata generator used for the upload. self.generator = generator #: Do the values support mastermix preparation? self.__support_mastermix = None #: The library to be screened. self.__library = None #: The parameter values (there must only be one for each parameter). self.__parameter_values = None self.__iso_conc = None self.__final_conc = None
def __init__(self, iso, single_stock_rack_map, pool_stock_rack_map=None, parent=None): """ Constructor. :param iso: The library creation ISO for which to generate the file. :type iso: :class:`thelma.entities.iso.StockSampleCreationIso` :param dict single_stock_rack_map: The barcodes for the destination rack for the single molecule design tube (these racks have to be empty). :param dict pool_stock_rack_map: The barcodes for the pool stock racks (these racks have to have empty tubes in defined positions). """ TxtWriter.__init__(self, parent=parent) self.iso = iso self.single_stock_rack_map = single_stock_rack_map self.pool_stock_rack_map = pool_stock_rack_map #: Sector preparation plates. self.__sector_prep_plate_map = None
def reset(self): TxtWriter.reset(self) self.__source_plates = dict()
def reset(self): TxtWriter.reset(self) self.__sector_prep_plate_map = dict()
def reset(self): TxtWriter.reset(self) self.tube_transfers = []