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, 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,
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 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,
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, 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, 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, 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, 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 __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,
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 __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, 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 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.__source_plates = dict()
def reset(self):
TxtWriter.reset(self)
self.__sector_prep_plate_map = dict()
def reset(self):
TxtWriter.reset(self)
self.tube_transfers = []
def reset(self):
TxtWriter.reset(self)
self.tube_transfers = []
