autoprotocol.instruction module¶

Contains all the Autoprotocol Instruction objects

copyright: 2018 by The Autoprotocol Development Team, see AUTHORS for more details.

license: BSD, see LICENSE for more details

class autoprotocol.instruction.Absorbance(object, wells, wavelength, dataref, flashes=25, incubate_before=None, temperature=None, settle_time=None)¶

Read the absorbance for the indicated wavelength for the indicated wells. Append an Absorbance instruction to the list of instructions for this Protocol object.

Parameters:

object (str or Ref) – Object to execute the absorbance read on
wells (list(Well) or WellGroup) – WellGroup of wells to be measured or a list of well references in the form of [“A1”, “B1”, “C5”, …]
wavelength (str or Unit) – wavelength of light absorbance to be read for the indicated wells
dataref (str) – name of this specific dataset of measured absorbances
flashes (int, optional) – number of flashes for the read
incubate_before (dict, optional) –
incubation prior to reading if desired

shaking: dict, optional

shake parameters if desired

amplitude: str or Unit

amplitude of shaking between 1 and 6:millimeter

orbital: bool

True for oribital and False for linear shaking

duration: str, Unit, optional

time prior to plate reading
temperature (str or Unit, optional) – set temperature to heat plate reading chamber
settle_time (str or Unit, optional) – time to pause before each well read

class autoprotocol.instruction.AcousticTransfer(groups, droplet_size)¶

Specify source and destination wells for transferring liquid via an acoustic liquid handler. Droplet size is usually device-specific.

Parameters:	groups (list(dict)) – List of transfer groups in the form of: { "transfer": [ { "to": "foo/A1", "from": "bar/A1", "volume": "1:nl" } ] } droplet_size (str or Unit) – Volume representing a droplet_size. The volume of each transfer should be a multiple of this volume.

class autoprotocol.instruction.Autopick(groups, criteria, dataref)¶

Pick colonies from the agar-containing location(s) specified in sources to the location(s) specified in dests in highest to lowest rank order until there are no more colonies available. If fewer than min_abort pickable colonies have been identified from the location(s) specified in sources, the run will stop and no further instructions will be executed.

Parameters:	groups (list(dict)) – Groups of colonies to pick and where to transport them to criteria (dict) – Dictionary of autopicking criteria. dataref (str) – Name of dataset to save the picked colonies to

class autoprotocol.instruction.CountCells(wells, volume, dataref, labels=None)¶

Count the number of cells in a sample that are positive/negative for a given set of labels.

Parameters:

wells (WellGroup) – List of wells that will be used for cell counting.
volume (Unit) – Volume that should be consumed from each well for the purpose of cell counting.
dataref (str) – Name of dataset that will be returned.
labels (list(string), optional) – Cells will be scored for presence or absence of each label in this list. If staining is required to visualize these labels, they must be added before execution of this instruction.

class autoprotocol.instruction.Cover(object, lid='standard', retrieve_lid=None)¶

Place specified lid type on specified container

Parameters:	object (str) – Container to be covered lid (Enum({'standard', 'universal', 'low_evaporation'}), optional) – Type of lid to cover container with retrieve_lid (bool) – Flag to retrieve lid from stored location

class autoprotocol.instruction.Dispense(object, columns, reagent=None, resource_id=None, reagent_source=None, step_size=None, flowrate=None, nozzle_position=None, pre_dispense=None, shape=None, shake_after=None)¶

Dispense specified reagent to specified columns. Only one of reagent, resource_id, and reagent_source can be specified for a given instruction.

Parameters:

object (Container or str) – Container for reagent to be dispensed to.
columns (list) – Columns to be dispensed to, in the form of a list of dicts specifying the column number and the volume to be dispensed to that column. Columns are indexed from 0. [{“column”: <column num>, “volume”: <volume>}, …]
reagent (str, optional) – Reagent to be dispensed.
resource_id (str, optional) – Resource to be dispensed.
reagent_source (Well, optional) – Aliquot to be dispensed from.
step_size (str or Unit, optional) – Specifies that the dispense operation must be executed using a pump that has a dispensing resolution of step_size.
flowrate (str or Unit, optional) – The rate at which the peristaltic pump should dispense in Units of flow rate, e.g. microliter/second.
nozzle_position (dict, optional) – A dict represent nozzle offsets from the center of the bottom of the plate’s well. see Dispense.builders.nozzle_position; specified as {“position_x”: Unit, “position_y”: Unit, “position_z”: Unit}.
pre_dispense (str or Unit, optional) – The volume of reagent to be dispensed per-nozzle into waste immediately prior to dispensing into the ref.
shape (dict, optional) – The shape of the dispensing head to be used for the dispense. See liquid_handle_builders.shape_builder; specified as {“rows”: int, “columns”: int, “format”: str} with format being a valid SBS format.
shake_after (dict, optional) – Parameters that specify how a plate should be shaken at the very end of the instruction execution. {“duration”: Unit, “frequency”: Unit, “path”: str, “amplitude”: Unit}

class autoprotocol.instruction.FlashFreeze(object, duration)¶

Flash freeze the contents of the specified container by submerging it in liquid nitrogen for the specified amount of time.

Parameters:	object (Container or str) – Container to be flash frozen. duration (str or Unit) – Duration to submerge specified container in liquid nitrogen.

class autoprotocol.instruction.FlowAnalyze(dataref, FSC, SSC, negative_controls, samples, colors=None, positive_controls=None)¶

Perform flow cytometry.The instruction will be executed within the voltage range specified for each channel, optimized for the best sample separation/distribution that can be achieved within these limits. The vendor will specify the device that this instruction is executed on and which excitation and emission spectra are available. At least one negative control is required, which will be used to define data acquisition parameters as well as to determine any autofluorescent properties for the sample set. Additional negative positive control samples are optional. Positive control samples will be used to optimize single color signals and, if desired, to minimize bleed into other channels.

For each sample this instruction asks you to specify the volume and/or captured_events. Vendors might also require captured_events in case their device does not support volumetric sample intake. If both conditions are supported, the vendor will specify if data will be collected only until the first one is met or until both conditions are fulfilled.

Example Usage:

Autoprotocol Output:

Parameters:

dataref (str) – Name of flow analysis dataset generated.

FSC (dict) –

Dictionary containing FSC channel parameters in the form of:

{
  "voltage_range": {
    "low": "230:volt",
    "high": "280:volt"
    },
  "area": true,             //default: true
  "height": true,           //default: true
  "weight": false           //default: false
}

SSC (dict) –

Dictionary of SSC channel parameters in the form of:

{
  "voltage_range": {
    "low": <voltage>,
    "high": <voltage>"
    },
  "area": true,             //default: true
  "height": true,           //default: false
  "weight": false           //default: false
}

negative_controls (list(dict)) –

List of negative control wells in the form of:

{
    "well": well,
    "volume": volume,
    "captured_events": integer,     // optional, default infinity
    "channel": [channel_name]
}

at least one negative control is required.

samples (list(dict)) –

List of samples in the form of:

{
    "well": well,
    "volume": volume,
    "captured_events": integer,     // optional, default infinity
}

at least one sample is required

colors (list(dict), optional) –

Optional list of colors in the form of:

[{
  "name": "FitC",
  "emission_wavelength": "495:nanometer",
  "excitation_wavelength": "519:nanometer",
  "voltage_range": {
    "low": <voltage>,
    "high": <voltage>
  },
  "area": true,             //default: true
  "height": false,          //default: false
  "weight": false           //default: false
}]

positive_controls : list(dict), optional

Optional list of positive control wells in the form of:

[{
    "well": well,
    "volume": volume,
    "captured_events": integer,     // optional, default infinity
    "channel": [channel_name],
    "minimize_bleed": [{            // optional
      "from": color,
      "to": [color]
    }]
}]

class autoprotocol.instruction.Fluorescence(object, wells, excitation, emission, dataref, flashes=25, incubate_before=None, temperature=None, gain=None, detection_mode=None, position_z=None, settle_time=None, lag_time=None, integration_time=None)¶

Read the fluorescence for the indicated wavelength for the indicated wells. Append a Fluorescence instruction to the list of instructions for this Protocol object.

Parameters:

object (str or Container) – object to execute the fluorescence read on
wells (list(Well) or WellGroup) – WellGroup of wells to be measured or a list of well references in the form of [“A1”, “B1”, “C5”, …]
excitation (str or Unit) – wavelength of light used to excite the wells indicated
emission (str or Unit) – wavelength of light to be measured for the indicated wells
dataref (str) – name of this specific dataset of measured absorbances
flashes (int, optional) – number of flashes for this read
incubate_before (dict, optional) –
incubation prior to reading if desired

shaking: dict, optional

shake parameters if desired

amplitude: str or Unit

amplitude of shaking between 1 and 6:millimeter

orbital: bool

True for oribital and False for linear shaking

duration: str, Unit, optional

time prior to plate reading
temperature (str or Unit, optional) – set temperature to heat plate reading chamber
gain (float, optional) – float between 0 and 1, multiplier of maximum signal amplification
detection_mode (str, optional) – set the detection mode of the optics, [“top”, “bottom”], defaults to vendor specified defaults.
position_z (dict, optional) –
distance from the optics to the surface of the plate transport, only valid for “top” detection_mode and vendor capabilities. Specified as either a set distance - “manual”, OR calculated from a WellGroup - “calculated_from_wells”. Only one position_z determination may be specified
```
position_z = {
    "manual": Unit
    - OR -
    "calculated_from_wells": []
}
```
manual (str, Unit, optional) – parameter available within “position_z” to set the distance from the optics to the plate transport.
calculated_from_wells (list, WellGroup, Well, optional) – parameter available within “position_z” to set the distance from the optics to the plate transport. If specified, the average optimal (maximal signal) distance will be chosen from the list of wells and applied to all measurements.
settle_time (Unit, optional) – the time before the start of the measurement, defaults to vendor specifications
lag_time (Unit, optional) – time between flashes and the start of the signal integration, defaults to vendor specifications
integration_time (Unit, optional) – duration of the signal recording, per Well, defaults to vendor specifications

class autoprotocol.instruction.GelPurify(objects, volume, matrix, ladder, dataref, extract)¶

Separate nucleic acids on an agarose gel and purify.

Parameters:

objects (list or WellGroup) – WellGroup of wells to be purified
volume (str or Unit) – Volume of sample required for analysis
dataref (str) – Name of this specific dataset of measurements
matrix (str) – Agarose concentration and number of wells on gel used for separation
ladder (str) – Size range of ladder to be used to compare band size to
dataref – Name of dataset containing fragment sizes returned

extract (list(dict)) –

"extract": [{
      "elution_volume": volume,
      "elution_buffer": string, "water" | "TE",
      "lane": int,
      "band_size_range": {
        "min_bp": int,
        "max_bp": int,
      },
      "destination": well
    },
    {...}]

class autoprotocol.instruction.GelSeparate(objects, volume, matrix, ladder, duration, dataref)¶

Separate nucleic acids on an agarose gel.

Parameters:

objects (list or WellGroup or Well) – List of wells or WellGroup containing wells to be separated on gel.
volume (str or Unit) – Volume of liquid to be transferred from each well specified to a lane of the gel.
matrix (str) – Matrix (gel) in which to gel separate samples
ladder (str) – Ladder by which to measure separated fragment size
duration (str or Unit) – Length of time to run current through gel.
dataref (str) – Name of this set of gel separation results.

class autoprotocol.instruction.IlluminaSeq(flowcell, lanes, sequencer, mode, index, library_size, dataref, cycles)¶

Load aliquots into specified lanes for Illumina sequencing. The specified aliquots should already contain the appropriate mix for sequencing and require a library concentration reported in ng/uL.

Parameters:

flowcell (str) – Flowcell designation: “SR” or ” “PE”

lanes (list(dict)) –

"lanes": [{
      "object": aliquot, Well,
      "library_concentration": decimal, // ng/uL
    },
    {...}]

sequencer (str) – Sequencer designation: “miseq”, “hiseq” or “nextseq”
mode (str) – Mode designation: “rapid”, “mid” or “high”
index (str) – Index designation: “single”, “dual” or “none”
library_size (integer) – Library size expressed as an integer of basepairs
dataref (str) – Name of sequencing dataset that will be returned.
cycles (Enum({"read_1", "read_2", "index_1", "index_2"})) – Parameter specific to Illuminaseq read-length or number of sequenced bases. Refer to the ASC for more details

class autoprotocol.instruction.ImagePlate(object, mode, dataref)¶

Capture an image of the specified container.

Parameters:	object (str) – Container to take image of mode (str) – Imaging mode (currently supported: “top”) dataref (str) – Name of data reference of resulting image

class autoprotocol.instruction.Incubate(object, where, duration, shaking=False, co2=0, target_temperature=None, shaking_params=None)¶

Store a sample in a specific environment for a given duration. Once the duration has elapsed, the sample will be returned to the ambient environment until it is next used in an instruction.

Parameters:

object (Ref or str) – The container to be incubated
where (Enum({"ambient", "warm_37", "cold_4", "cold_20", "cold_80"})) – Temperature at which to incubate specified container
duration (Unit or str) – Length of time to incubate container
shaking (bool, optional) – Specify whether or not to shake container if available at the specified temperature
target_temperature (Unit or str, optional) – Specify a target temperature for a device (eg. an incubating block) to reach during the specified duration.
shaking_params (dict, optional) – Specify “path” and “frequency” of shaking parameters to be used with compatible devices (eg. thermoshakes)
co2 (int, optional) – Carbon dioxide percentage

class autoprotocol.instruction.Instruction(op, data)¶

Base class for an instruction that is to later be encoded as JSON.

json()¶

Return instruction object properly encoded as JSON for Autoprotocol.

Returns:	Instruction object encoded as json string
Return type:	str

class autoprotocol.instruction.LiquidHandle(locations, shape=None, mode=None, mode_params=None)¶

Manipulates liquids within locations

A liquid handle instruction is constructed as a list of locations, where each location consists of the well location and the tip transports carried out within the well.

Each liquid handle instruction corresponds to a single tip or set of tips.

Parameters:	locations (list(dict)) – See Also LiquidHandle.builders.location shape (dict, optional) – See Also LiquidHandle.builders.shape mode (str, optional) – the liquid handling mode mode_params (dict, optional) – See Also LiquidHandle.builders.instruction_mode_params

class autoprotocol.instruction.Luminescence(object, wells, dataref, incubate_before=None, temperature=None, settle_time=None, integration_time=None)¶

Read luminesence of indicated wells

Parameters:

object (str or Container) – object to execute the luminescence read on
wells (list or WellGroup) – WellGroup or list of wells to be measured
dataref (str) – name which dataset will be saved under
incubate_before (dict, optional) –
incubation prior to reading if desired

shaking: dict, optional

shake parameters if desired

amplitude: str or Unit

amplitude of shaking between 1 and 6:millimeter

orbital: bool

True for oribital and False for linear shaking

duration: str, Unit, optional

time prior to plate reading
temperature (str or Unit, optional) – set temperature to heat plate reading chamber
settle_time (str or Unit, optional) – time to pause before each well read
integration_time (Unit, optional) – duration of the signal recording, per Well, defaults to vendor specifications

class autoprotocol.instruction.MagneticTransfer(groups, head_type)¶

A magnetic_transfer instruction is constructed as a list of lists of groups, executed in order, where each group is a collect, release, dry, incubate, or mix sub-operation. These sub-operations control the behavior of tips which can be magnetized, and a heating platform. Groups in the same list of groups use the same tips.

Parameters:

groups (list(dict)) –
dict in the groups should belong to one of the following categories:

collect:

Collects beads from the specified “object” by raising and lowering magnetized tips repeatedly with an optional pause at well bottom.

release:

Release beads from unmagnetized tips by oscillating the tips vertically into and out of the “object”.

dry:

Dry beads on magnetized tips above and outside the “object”.

incubate:

Incubate the “object”.

mix:

Oscillate the tips into and out of the “object”
head_type (str) – Head-type used for this instruction

class autoprotocol.instruction.MeasureConcentration(object, volume, dataref, measurement)¶

Measure the concentration of DNA, ssDNA, RNA or Protein in the specified volume of the source aliquots.

Parameters:	object (list or WellGroup) – WellGroup of wells to be measured volume (str or Unit) – Volume of sample required for analysis dataref (str) – Name of this specific dataset of measurements measurement (str) – Class of material to be measured. One of [“DNA”, “ssDNA”, “RNA”, “protein”].

class autoprotocol.instruction.MeasureMass(object, dataref)¶

Measure the mass of containers

Parameters:	object (Container) – Container ref dataref (str) – Name of the data for the measurement

class autoprotocol.instruction.MeasureVolume(object, dataref)¶

Measure the mass of containers

Parameters:	object (list(Container)) – list of containers dataref (str) – Name of the data for the measurement

class autoprotocol.instruction.Oligosynthesize(oligos)¶

Parameters:

oligos (list of dicts) –

List of oligonucleotides to synthesize. Each dictionary should contain the oligo’s sequence, destination, scale and purification

[
    {
      "destination": "my_plate/A1",
      "sequence": "GATCRYMKSWHBVDN",
        // - standard IUPAC base codes
        // - IDT also allows rX (RNA), mX (2' O-methyl RNA), and
        //   X*/rX*/mX* (phosphorothioated)
        // - they also allow inline annotations for modifications,
        //   eg "GCGACTC/3Phos/" for a 3' phosphorylation
        //   eg "aggg/iAzideN/cgcgc" for an internal modification
      "scale": "25nm" | "100nm" | "250nm" | "1um",
      "purification": "standard" | "page" | "hplc",
        // default: standard
    },
    ...
]

class autoprotocol.instruction.Provision(resource_id, dests)¶

Provision a commercial resource from a catalog into the specified destination well(s). A new tip is used for each destination well specified to avoid contamination.

Parameters:	resource_id (str) – Resource ID from catalog. dests (list(dict)) – Destination(s) for specified resource, together with volume information
Raises:	`TypeError` – If resource_id is not a string. `RuntimeError` – If length of the list of volumes specified does not match the number of destination wells specified. `TypeError` – If volume is not specified as a string or Unit (or a list of either)

class autoprotocol.instruction.SangerSeq(object, wells, dataref, type, primer=None)¶

Send the indicated wells of the container specified for Sanger sequencing. The specified wells should already contain the appropriate mix for sequencing, including primers and DNA according to the instructions provided by the vendor.

Parameters:

object (Container or str) – Container with well(s) that contain material to be sequenced.
wells (list(str)) – Well indices of the container that contain appropriate materials to be sent for sequencing.
dataref (str) – Name of sequencing dataset that will be returned.
type (Enum({"standard", "rca"})) – Sanger sequencing type
primer (Container, optional) – Tube containing sufficient primer for all RCA reactions. This field will be ignored if you specify the sequencing type as “standard”. Tube containing sufficient primer for all RCA reactions

class autoprotocol.instruction.Seal(object, type='ultra-clear', mode=None, mode_params=None)¶

Seal indicated container using the automated plate sealer.

Parameters:

object (Ref or str) – Container to be sealed
type (str, optional) – Seal type to be used (optional)
mode (str, optional) – Method used to seal plate (optional). “thermal” or “adhesive”
mode_params (dict, optional) –
Thermal sealing parameters

temperature : str, optional

Temperature to seal plate at

duration : str, optional

Duration for which to apply heated sealing plate onto ref

class autoprotocol.instruction.Spectrophotometry(dataref, object, groups, interval=None, num_intervals=None, temperature=None, shake_before=None)¶

Execute a Spectrophotometry plate read on the obj.

Parameters:

dataref (str) – Name of the resultant dataset to be returned.
object (Container or str) – Container to be read.
groups (list) – A list of groups generated by SpectrophotometryBuilders groups builders, any of absorbance_mode_params, fluorescence_mode_params, luminescence_mode_params, or shake_mode_params.
interval (Unit or str, optional) – The time between each of the read intervals.
num_intervals (int, optional) – The number of times that the groups should be executed.
temperature (Unit or str, optional) – The temperature that the entire instruction should be executed at.
shake_before (dict, optional) – A dict of params generated by SpectrophotometryBuilders.shake_before that dictates how the obj should be incubated with shaking before any of the groups are executed.

class autoprotocol.instruction.Spin(object, acceleration, duration, flow_direction=None, spin_direction=None)¶

Apply the specified amount of acceleration to a plate using a centrifuge.

Parameters:

object (Ref or str) – Container to be centrifuged.
acceleration (str) – Amount of acceleration to be applied to the container, expressed in units of “g” or “meter/second^2”
duration (str or Unit) – Amount of time to apply acceleration.
flow_direction (str) – Specifies the direction contents will tend toward with respect to the container. Valid directions are “inward” and “outward”, default value is “inward”.
spin_direction (list(str)) – A list of “cw” (clockwise), “cww” (counterclockwise). For each element in the list, the container will be spun in the stated direction for the set “acceleration” and “duration”. Default values are derived from the “flow_direction”. If “flow_direction” is “outward”, then “spin_direction” defaults to [“cw”, “ccw”]. If “flow_direction” is “inward”, then “spin_direction” defaults to [“cw”].

class autoprotocol.instruction.Thermocycle(object, groups, volume='25:microliter', dataref=None, dyes=None, melting_start=None, melting_end=None, melting_increment=None, melting_rate=None, lid_temperature=None)¶

Append a Thermocycle instruction to the list of instructions, with groups being a list of dicts in the form of:

"groups": [{
    "cycles": integer,
    "steps": [{
      "duration": duration,
      "temperature": temperature,
      "read": boolean // optional (default true)
    },{
      "duration": duration,
      "gradient": {
        "top": temperature,
        "bottom": temperature
      },
      "read": boolean // optional (default true)
    }]
}],

To specify a melting curve, all four melting-relevant parameters must have a value.

Parameters:

object (str or Ref) – Container to be thermocycled
groups (list(dict)) – List of thermocycling instructions formatted as above
volume (str or Unit, optional) – Volume contained in wells being thermocycled
dataref (str, optional) – Name of dataref representing read data if performing qPCR
dyes (dict, optional) – Dictionary mapping dye types to the wells they’re used in
melting_start (str or Unit) – Temperature at which to start the melting curve.
melting_end (str or Unit) – Temperature at which to end the melting curve.
melting_increment (str or Unit) – Temperature by which to increment the melting curve. Accepted increment values are between 0.1 and 9.9 degrees celsius.
melting_rate (str or Unit) – Specifies the duration of each temperature step in the melting curve.
lid_temperature (str or Unit) – Specifies the lid temperature throughout the duration of the instruction

Raises:

ValueError – If one of dataref and dyes is specified but the other isn’t.
ValueError – If all melting curve-related parameters are specified but dyes isn’t.
ValueError – If some melting curve-related parameteres are specified but not all of them.
ValueError – If invalid dyes are supplied.

static convert_well_map_to_dye_map(well_map)¶

Take a map of wells to the dyes it contains and returns a map of dyes to the list of wells that contain it.

well_map - [{well:str}]

static find_invalid_dyes(dyes)¶

Take a set or list of dye names and returns the set that are not valid.

dyes - [list or set]

class autoprotocol.instruction.Uncover(object, store_lid=None)¶

Remove lid from specified container

Parameters:	object (str) – Container to remove lid from store_lid (bool) – Flag to store the uncovered lid

class autoprotocol.instruction.Unseal(object)¶

Remove seal from indicated container using the automated plate unsealer.

Parameters:	object (Ref or str) – Container to be unsealed