def __calculate_single_stock_transfer_volume(self):
# Determines the volume that has to be transferred from a single design
# stock tube to a future pool stock tube (for the given volume,
# concentration, and number of designs). The target volume might
# be increased if the resulting single design transfer volume has
# more than 1 decimal place.
# :raises ValueErrors: if something the values are not compatible
target_single_conc = float(self.__target_concentration) \
/ self.__number_designs
if target_single_conc > self.__stock_concentration:
msg = 'The requested target concentration (%i nM) cannot be ' \
'achieved since it would require a concentration of %s nM ' \
'for each single design in the pool. However, the stock ' \
'concentration for this design type is only %s nM.' \
% (self.__target_concentration,
get_trimmed_string(target_single_conc),
get_trimmed_string(self.__stock_concentration))
raise ValueError(msg)
dil_factor = self.__stock_concentration / target_single_conc
min_target_volume = round_up(dil_factor *
self.__min_cybio_transfer_vol)
if (min_target_volume > self.__target_volume):
msg = 'The target volume you have requested (%i ul) is too low ' \
'for the required dilution (1:%s) since the CyBio cannot ' \
'pipet less than %.1f ul per transfer. The volume that has ' \
'to be taken from the stock for each single molecule ' \
'design would be lower that that. Increase the target ' \
'volume to %.1f ul or increase the target concentration.' \
% (self.__target_volume, get_trimmed_string(dil_factor),
self.__min_cybio_transfer_vol,
round_up(min_target_volume, 0))
raise ValueError(msg)
self.__stock_transfer_vol = round_up(self.__target_volume / dil_factor)
self.__adjusted_target_vol = round(
self.__stock_transfer_vol * dil_factor, 1)
# must be at least 1 ul according to the last check
total_transfer_vol = self.__stock_transfer_vol * self.__number_designs
if total_transfer_vol > self.__target_volume:
msg = 'The target volume you have requested (%i ul) is too low ' \
'for the concentration you have ordered (%i uM) since it ' \
'would require already %s ul per molecule design (%s ul in ' \
'total) to achieve the requested concentration. Increase ' \
'the volume or lower the concentration, please.' \
% (self.__target_volume, self.__target_concentration,
get_trimmed_string(self.__stock_transfer_vol),
get_trimmed_string(total_transfer_vol))
raise ValueError(msg)
def __store_line_value(self, dil_info, total_vol, pos_label):
"""
Stores the values for one line.
"""
dil_info = dil_info.strip()
info_tokens = dil_info.split(' (')
final_dil_factor = float(info_tokens[1][:-1])
initial_dil_factor = TransfectionParameters.\
calculate_initial_reagent_dilution(final_dil_factor)
reagent_vol = round_up((total_vol / initial_dil_factor))
total_vol = reagent_vol * initial_dil_factor
total_vol = round(total_vol, 1)
diluent_vol = total_vol - reagent_vol
initial_dil_factor = round(initial_dil_factor, 1)
self.__position_values.append(pos_label)
self.__name_values.append(info_tokens[0])
self.__final_dil_factor_values.append(
get_trimmed_string(final_dil_factor))
self.__ini_dil_factor_values.append(
get_trimmed_string(initial_dil_factor))
self.__total_volume_values.append(get_trimmed_string(total_vol))
self.__reagent_volume_values.append(get_trimmed_string(reagent_vol))
self.__diluent_volume_values.append(get_trimmed_string(diluent_vol))
def __store_line_value(self, dil_info, total_vol, pos_label):
"""
Stores the values for one line.
"""
dil_info = dil_info.strip()
info_tokens = dil_info.split(' (')
final_dil_factor = float(info_tokens[1][:-1])
initial_dil_factor = TransfectionParameters.\
calculate_initial_reagent_dilution(final_dil_factor)
reagent_vol = round_up((total_vol / initial_dil_factor))
total_vol = reagent_vol * initial_dil_factor
total_vol = round(total_vol, 1)
diluent_vol = total_vol - reagent_vol
initial_dil_factor = round(initial_dil_factor, 1)
self.__position_values.append(pos_label)
self.__name_values.append(info_tokens[0])
self.__final_dil_factor_values.append(
get_trimmed_string(final_dil_factor))
self.__ini_dil_factor_values.append(
get_trimmed_string(initial_dil_factor))
self.__total_volume_values.append(get_trimmed_string(total_vol))
self.__reagent_volume_values.append(get_trimmed_string(reagent_vol))
self.__diluent_volume_values.append(get_trimmed_string(diluent_vol))
def __calculate_single_stock_transfer_volume(self):
# Determines the volume that has to be transferred from a single design
# stock tube to a future pool stock tube (for the given volume,
# concentration, and number of designs). The target volume might
# be increased if the resulting single design transfer volume has
# more than 1 decimal place.
# :raises ValueErrors: if something the values are not compatible
target_single_conc = float(self.__target_concentration) \
/ self.__number_designs
if target_single_conc > self.__stock_concentration:
msg = 'The requested target concentration (%i nM) cannot be ' \
'achieved since it would require a concentration of %s nM ' \
'for each single design in the pool. However, the stock ' \
'concentration for this design type is only %s nM.' \
% (self.__target_concentration,
get_trimmed_string(target_single_conc),
get_trimmed_string(self.__stock_concentration))
raise ValueError(msg)
dil_factor = self.__stock_concentration / target_single_conc
min_target_volume = round_up(dil_factor * self.__min_cybio_transfer_vol)
if (min_target_volume > self.__target_volume):
msg = 'The target volume you have requested (%i ul) is too low ' \
'for the required dilution (1:%s) since the CyBio cannot ' \
'pipet less than %.1f ul per transfer. The volume that has ' \
'to be taken from the stock for each single molecule ' \
'design would be lower that that. Increase the target ' \
'volume to %.1f ul or increase the target concentration.' \
% (self.__target_volume, get_trimmed_string(dil_factor),
self.__min_cybio_transfer_vol,
round_up(min_target_volume, 0))
raise ValueError(msg)
self.__stock_transfer_vol = round_up(self.__target_volume / dil_factor)
self.__adjusted_target_vol = round(
self.__stock_transfer_vol * dil_factor, 1)
# must be at least 1 ul according to the last check
total_transfer_vol = self.__stock_transfer_vol * self.__number_designs
if total_transfer_vol > self.__target_volume:
msg = 'The target volume you have requested (%i ul) is too low ' \
'for the concentration you have ordered (%i uM) since it ' \
'would require already %s ul per molecule design (%s ul in ' \
'total) to achieve the requested concentration. Increase ' \
'the volume or lower the concentration, please.' \
% (self.__target_volume, self.__target_concentration,
get_trimmed_string(self.__stock_transfer_vol),
get_trimmed_string(total_transfer_vol))
raise ValueError(msg)
def get_source_plate_transfer_volume():
"""
Returns the volume that is transferred from a pool stock rack to a
library source (preparation) plate in ul.
"""
dilution_factor = float(POOL_STOCK_RACK_CONCENTRATION) \
/ PREPARATION_PLATE_CONCENTRATION
vol = PREPARATION_PLATE_VOLUME / dilution_factor
return round_up(vol)
def __split_into_transferable_amounts(self, planned_transfer):
# Checks whether the volume is larger than the allowed maximum
# transfer volume and splits it into transferable amounts.
volume = round(planned_transfer.volume * VOLUME_CONVERSION_FACTOR, 1)
if volume <= self._max_transfer_volume:
return [volume]
self.__has_split_volumes = True
no_volumes = ceil(volume / self._max_transfer_volume)
amounts = []
partial_vol = round_up((volume / no_volumes), 1)
while volume > 0:
if volume < partial_vol:
amounts.append(volume)
volume = 0
else:
amounts.append(partial_vol)
volume = volume - partial_vol
amounts.sort()
return amounts
def __split_into_transferable_amounts(self, planned_transfer):
# Checks whether the volume is larger than the allowed maximum
# transfer volume and splits it into transferable amounts.
volume = round(planned_transfer.volume * VOLUME_CONVERSION_FACTOR, 1)
if volume <= self._max_transfer_volume:
return [volume]
self.__has_split_volumes = True
no_volumes = ceil(volume / self._max_transfer_volume)
amounts = []
partial_vol = round_up((volume / no_volumes), 1)
while volume > 0:
if volume < partial_vol:
amounts.append(volume)
volume = 0
else:
amounts.append(partial_vol)
volume = volume - partial_vol
amounts.sort()
return amounts
def calculate_iso_volume(cls, number_target_wells, number_replicates,
iso_reservoir_spec, optimem_dil_factor,
pipetting_specs):
"""
Calculates the ISO volume required to fill the given number
of target wells (assuming the given number of interplate replicates).
:param number_target_wells: The number of target wells in all
design racks of an experiment design.
:type number_target_wells: :class:`int`
:param number_replicates: The number of replicates.
:type number_replicates: :class:`int`
:param optimem_dil_factor: The optimem dilution factor depends on
molecule type or final concentration.
:type optimem_dil_factor: positive number
:param iso_reservoir_spec: The reservoir specs to be assumed.
:type iso_reservoir_spec:
:class:`thelma.entities.liquidtransfer.ReservoirSpecs`
:return: The ISO volume that should be ordered in the ISO to generate
an sufficient amount of mastermix solution.
:param pipetting_specs: Defines whether to use a static dead volume
or a dynamic (represents Biomek-transfer).
:type pipetting_specs: :class:`PipettingSpecs`
"""
required_volume = cls.\
calculate_mastermix_volume_from_target_well_number(
number_target_wells, number_replicates, iso_reservoir_spec,
pipetting_specs)
iso_volume = required_volume / (cls.REAGENT_MM_DILUTION_FACTOR \
* optimem_dil_factor)
min_volume = get_min_transfer_volume(pipetting_specs)
if iso_volume < min_volume: iso_volume = min_volume
return round_up(iso_volume)
def calculate_iso_volume(cls, number_target_wells, number_replicates,
iso_reservoir_spec, optimem_dil_factor,
pipetting_specs):
"""
Calculates the ISO volume required to fill the given number
of target wells (assuming the given number of interplate replicates).
:param number_target_wells: The number of target wells in all
design racks of an experiment design.
:type number_target_wells: :class:`int`
:param number_replicates: The number of replicates.
:type number_replicates: :class:`int`
:param optimem_dil_factor: The optimem dilution factor depends on
molecule type or final concentration.
:type optimem_dil_factor: positive number
:param iso_reservoir_spec: The reservoir specs to be assumed.
:type iso_reservoir_spec:
:class:`thelma.entities.liquidtransfer.ReservoirSpecs`
:return: The ISO volume that should be ordered in the ISO to generate
an sufficient amount of mastermix solution.
:param pipetting_specs: Defines whether to use a static dead volume
or a dynamic (represents Biomek-transfer).
:type pipetting_specs: :class:`PipettingSpecs`
"""
required_volume = cls.\
calculate_mastermix_volume_from_target_well_number(
number_target_wells, number_replicates, iso_reservoir_spec,
pipetting_specs)
iso_volume = required_volume / (cls.REAGENT_MM_DILUTION_FACTOR \
* optimem_dil_factor)
min_volume = get_min_transfer_volume(pipetting_specs)
if iso_volume < min_volume: iso_volume = min_volume
return round_up(iso_volume)
