transcriptic.objects

Project

class transcriptic.objects.Project(project_id, attributes=None, connection=None)

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)
id

str – Project id

name

str – Project name

attributes

dict – Master attributes dictionary

connection

transcriptic.config.Connection – Transcriptic Connection object associated with this specific object

Project.runs()

Project.runs(use_cache=True)

Get the list of runs belonging to the project

Parameters:use_cache (Boolean) – Determines whether the cached list of runs is returned
Returns:Returns a DataFrame of runs, with the id and title as columns
Return type:DataFrame

Project.submit()

Project.submit(protocol, title, test_mode=False)

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

Run

class transcriptic.objects.Run(run_id, attributes=None, connection=None, timeout=30.0)

Bases: transcriptic.objects._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]
id

str – Run id

name

str – Run name

data

DataFrame – DataFrame summary of all datasets which belong to this run

instructions

DataFrame – DataFrame summary of all Instruction objects which belong to this run

containers

DataFrame – DataFrame summary of all Container objects which belong to this run

project_id

str – Project id which run belongs to

attributes

dict – Master attributes dictionary

connection

transcriptic.config.Connection – Transcriptic Connection object associated with this specific object

Containers

Helper for allowing direct access of Container objects

Returns:Returns a Series of Container objects
Return type:Series
Datasets

Helper for allowing direct access of Dataset objects

Returns:Returns a Series of Dataset objects
Return type:Series
Instructions

Helper for allowing direct access of Instruction objects

Returns:Returns a Series of Instruction objects
Return type:Series
containers
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
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
instructions

Dataset

class transcriptic.objects.Dataset(data_id, attributes=None, connection=None)

Bases: transcriptic.objects._BaseObject

A Dataset object contains helper methods for accessing data related information

id

str – Dataset id

name

str – Dataset name

data

DataFrame – DataFrame of well-indexed data values. Note that associated metadata is found in attributes dictionary

container

Container – Container object that was used for this dataset

operation

str – Operation used for generating the dataset

data_type

str – Data type of this dataset

attributes

dict – Master attributes dictionary

connection

transcriptic.config.Connection – Transcriptic Connection object associated with this specific object

cross_ref_aliquots()
data
raw_data

Instruction

class transcriptic.objects.Instruction(attributes, connection=None)

Bases: future.types.newobject.newobject

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 explicity.

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
id

str – Instruction id

name

str – Instruction name

warps

DataFrame – DataFrame of warps in the instruction

started_at

str – Time where instruction begun

completed_at

str – Time where instruction ended

device_id

str – Id of device which instruction was executed on

attributes

dict – Master attributes dictionary

connection

transcriptic.config.Connection – Transcriptic Connection object associated with this specific object

monitoring(data_type='pressure', grouping=None)

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

Return type:

DataFrame

warps

Container

class transcriptic.objects.Container(container_id, attributes=None, connection=None)

Bases: transcriptic.objects._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)
name

str – Name of container

well_map

dict – Well mapping with well indices for keys and well names as values

aliquots

DataFrame – DataFrame of aliquots present in the container. DataFrame index now corresponds to the Well Index.

container_type

autoprotocol.container_type.ContainerType – Autoprotocol ContainerType object with many useful container type information and functions.

cover

str – Cover type of container

storage

str – 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)
__repr__()

Return a string representation of a Container using the specified name. (ex. Container(‘my_plate’))

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.