transcriptic.jupyter¶
Project¶
-
class
transcriptic.jupyter.
Project
(project_id, attributes=None, connection=None)[source]¶ A Project object contains helper methods for managing your runs. You can view the runs associated with this project as well as submit runs to the project.
Example Usage:
myProject = Project("My Project") projectRuns = myProject.runs() myRunId = projectRuns.query("title == 'myRun'").id.item() myRun = Run(myRunId)
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id
¶ Project id
- Type
str
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name
¶ Project name
- Type
str
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attributes
¶ Master attributes dictionary
- Type
dict
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connection
¶ Transcriptic Connection object associated with this specific object
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Project.runs()¶
Project.submit()¶
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Project.
submit
(protocol, title, test_mode=False)[source]¶ Submit a run to this project
- Parameters
protocol (dict) – Autoprotocol Protocol in dictionary form, can be generated using Protocol.as_dict()
title (Optional[str]) – Title of run. Run-id will automatically be used as name if field is not provided
test_mode (Optional[boolean]) – Determines if run will be submitted will be treated as a test run or a run that is meant for execution
- Returns
Returns a run object if run is successfully submitted
- Return type
Run¶
-
class
transcriptic.jupyter.
Run
(run_id, attributes=None, connection=None, timeout=30.0)[source]¶ Bases:
transcriptic.jupyter.common._BaseObject
A Run object contains helper methods for accessing Run-related information such as Instructions, Datasets and monitoring data.
Example Usage:
myRun = Run('r12345') myRun.data myRun.instructions myRun.containers myRun.Instructions[0]
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id
¶ Run id
- Type
str
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name
¶ Run name
- Type
str
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data
¶ DataFrame summary of all datasets which belong to this run
- Type
DataFrame
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instructions
¶ DataFrame summary of all Instruction objects which belong to this run
- Type
DataFrame
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containers
¶ DataFrame summary of all Container objects which belong to this run
- Type
DataFrame
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project_id
¶ Project id which run belongs to
- Type
str
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attributes
¶ Master attributes dictionary
- Type
dict
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connection
¶ Transcriptic Connection object associated with this specific object
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property
Containers
¶ Helper for allowing direct access of Container objects
- Returns
Returns a Series of Container objects
- Return type
Series
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property
Datasets
¶ Helper for allowing direct access of Dataset objects
- Returns
Returns a Series of Dataset objects
- Return type
Series
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property
Instructions
¶ Helper for allowing direct access of Instruction objects
- Returns
Returns a Series of Instruction objects
- Return type
Series
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property
containers
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property
data
Find and generate a list of Dataset objects which are associated with this run
- Returns
Returns a DataFrame of datasets, with Name, Dataset and DataType as columns
- Return type
DataFrame
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property
data_ids
¶ Find and generate a list of datarefs and data_ids associated with this run.
- Returns
Returns a DataFrame of data ids, with datarefs and data_ids as columns
- Return type
DataFrame
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property
instructions
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Dataset¶
-
class
transcriptic.jupyter.
Dataset
(data_id, attributes=None, connection=None)[source]¶ Bases:
transcriptic.jupyter.common._BaseObject
A Dataset object contains helper methods for accessing data related information
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id
¶ Dataset id
- Type
str
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name
¶ Dataset name
- Type
str
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data
¶ - DataFrame of well-indexed data values. Note that associated metadata is found in
attributes dictionary
- Type
DataFrame
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attachments
¶ names and data of all attachments for the dataset
- Type
dict(str, bytes)
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operation
¶ Operation used for generating the dataset
- Type
str
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data_type
¶ Data type of this dataset
- Type
str
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attributes
¶ Master attributes dictionary
- Type
dict
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connection
¶ Transcriptic Connection object associated with this specific object
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property
attachments
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property
data
-
data_objects
()[source]
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property
raw_data
¶
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Instruction¶
-
class
transcriptic.jupyter.
Instruction
(attributes, connection=None)[source]¶ Bases:
object
An Instruction object contains information related to the current instruction such as the start, completed time as well as warps associated with the instruction.
Note that Instruction objects are usually created as part of a run and not created explicitly.
Additionally, if diagnostic information is available, one can click on the Show Diagnostics Data button to view relevant diagnostic information.
Example Usage:
myRun = Run('r12345') myRun.instructions # Access instruction object myRun.Instructions[1] myRun.Instructions[1].warps
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id
¶ Instruction id
- Type
str
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name
¶ Instruction name
- Type
str
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warps
¶ DataFrame of warps in the instruction
- Type
DataFrame
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started_at
¶ Time where instruction begun
- Type
str
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completed_at
¶ Time where instruction ended
- Type
str
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device_id
¶ Id of device which instruction was executed on
- Type
str
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attributes
¶ Master attributes dictionary
- Type
dict
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connection
¶ Transcriptic Connection object associated with this specific object
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monitoring
(data_type='pressure', grouping=None)[source]¶ View monitoring data of a given instruction
- Parameters
data_type (Optional[str]) – Monitoring data type, defaults to ‘pressure’
grouping (Optional[str]) – Determines whether the values will be grouped, defaults to None. E.g. “5:ms”
- Returns
Returns a pandas dataframe of the monitoring data if present. Returns an empty dataframe if no data can be found due to errors.
- Return type
DataFrame
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property
warp_events
¶ Warp events include discrete monitoring events such as liquid sensing events for a particular instruction.
-
property
warps
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Container¶
-
class
transcriptic.jupyter.
Container
(container_id, attributes=None, connection=None)[source]¶ Bases:
transcriptic.jupyter.common._BaseObject
A Container object represents a container from the Transcriptic LIMS and contains relevant information on the container type as well as the aliquots present in the container.
- Example Usage:
my_container = container("ct186apgz6a374") my_container.well_map my_container.aliquots my_container.container_type.col_count my_container.container_type.robotize("B1") my_container.container_type.humanize(12)
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name
¶ Name of container
- Type
str
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well_map
¶ Well mapping with well indices for keys and well names as values
- Type
dict
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aliquots
¶ DataFrame of aliquots present in the container. DataFrame index now corresponds to the Well Index.
- Type
DataFrame
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container_type
¶ Autoprotocol ContainerType object with many useful container type information and functions.
- Type
autoprotocol.container_type.ContainerType
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cover
¶ Cover type of container
- Type
str
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storage
¶ Storage condition of container
Example Usage:
my_container = container("ct186apgz6a374") my_container.well_map my_container.container_type.col_count my_container.container_type.robotize("B1") my_container.container_type.humanize(12)
- Type
str
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__repr__
()[source]¶ Return a string representation of a Container using the specified name. (ex. Container(‘my_plate’))
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property
aliquots
Return a DataFrame of aliquots in the container, along with aliquot name, volume, and properties. Row index for the DataFrame corresponds to the well index of the aliquot.