BLRun package

BEELINE Run (BLRun) module contains the following main class:

• BLRun.BLRun and three additional classes used in the definition of BLRun class
• BLRun.ConfigParser
• BLRun.InputSettings
• BLRun.OutputSettings

class BLRun.BLRun(input_settings: BLRun.InputSettings, output_settings: BLRun.OutputSettings)

Bases: object

The BLRun object is created by parsing a user-provided configuration file. Its methods provide for further processing its inputs into a series of jobs to be run, as well as running these jobs.

execute_runners(parallel=False, num_threads=1)

Run each of the algorithms

class BLRun.ConfigParser

Bases: object

Define static methods for parsing a config file that sets a large number of parameters for the pipeline

static parse(config_file_handle) → BLRun.BLRun

class BLRun.InputSettings(datadir, datasets, algorithms)

Bases: object

class BLRun.OutputSettings(base_dir, output_prefix: pathlib.Path)

Bases: object

Structure for storing the names of directories that output should be written to

Submodules

BLRun.genie3Runner module

BLRun.genie3Runner.generateInputs(RunnerObj)

Function to generate desired inputs for GENIE3. If the folder/files under RunnerObj.datadir exist, this function will not do anything.

Parameters:RunnerObj – An instance of the BLRun

BLRun.genie3Runner.parseOutput(RunnerObj)

Function to parse outputs from GENIE3.

Parameters:RunnerObj – An instance of the BLRun

BLRun.genie3Runner.run(RunnerObj)

Function to run GENIE3 algorithm

Parameters:RunnerObj – An instance of the BLRun

BLRun.grisliRunner module

BLRun.grisliRunner.generateInputs(RunnerObj)

Function to generate desired inputs for GRISLI. If the folder/files under RunnerObj.datadir exist, this function will not do anything.

BLRun.grisliRunner.parseOutput(RunnerObj)

Function to parse outputs from GRISLI.

BLRun.grisliRunner.run(RunnerObj)

Function to run GRISLI algorithm

BLRun.grnboost2Runner module

BLRun.grnboost2Runner.generateInputs(RunnerObj)

Function to generate desired inputs for GRNBoost2. If the folder/files under RunnerObj.datadir exist, this function will not do anything.

BLRun.grnboost2Runner.parseOutput(RunnerObj)

Function to parse outputs from GRNBOOST2.

BLRun.grnboost2Runner.run(RunnerObj)

Function to run GRNBOOST2 algorithm

BLRun.grnvbemRunner module

BLRun.grnvbemRunner.generateInputs(RunnerObj)

Function to generate desired inputs for GRNVBEM. It will create the input folder at RunnerObj.dataset.name/GRNVBEM/ if it does not exist already. The input folder will contain an ExpressionData.csv with cells ordered according to the pseudotime along the columns, and genes along the rows. If the files already exist, this function will overwrite it.

BLRun.grnvbemRunner.parseOutput(RunnerObj)

Function to parse outputs from GRNVBEM.

BLRun.grnvbemRunner.run(RunnerObj)

Function to run GRN-VBEM algorithm

BLRun.jump3Runner module

BLRun.jump3Runner.generateInputs(RunnerObj)

Function to generate desired inputs for JUMP3. If the folder/files under RunnerObj.datadir exist, this function will not do anything.

BLRun.jump3Runner.parseOutput(RunnerObj)

Function to parse outputs from JUMP3.

BLRun.jump3Runner.run(RunnerObj)

Function to run GRN-VBEM algorithm

BLRun.leapRunner module

BLRun.leapRunner.generateInputs(RunnerObj)

If the folder/files under RunnerObj.datadir exist, this function will not do anything.

BLRun.leapRunner.parseOutput(RunnerObj)

Function to parse outputs from LEAP.

BLRun.leapRunner.run(RunnerObj)

Function to run LEAP algorithm

Requires the maxLag parameter

BLRun.pidcRunner module

BLRun.pidcRunner.generateInputs(RunnerObj)

Function to generate desired inputs for SCODE. If the folder/files under RunnerObj.datadir exist, this function will not do anything.

BLRun.pidcRunner.parseOutput(RunnerObj)

Function to parse outputs from SCODE.

BLRun.pidcRunner.run(RunnerObj)

Function to run PIDC algorithm

BLRun.ppcorRunner module

BLRun.ppcorRunner.generateInputs(RunnerObj)

Function to generate desired inputs for PPCOR. If the folder/files under RunnerObj.datadir exist, this function will not do anything.

BLRun.ppcorRunner.parseOutput(RunnerObj)

Function to parse outputs from PPCOR.

BLRun.ppcorRunner.run(RunnerObj)

Function to run PPCOR algorithm

BLRun.runner module

class BLRun.runner.Runner(params)

Bases: object

A runnable analysis to be incorporated into the pipeline

generateInputs()

parseOutput()

run()

BLRun.scingeRunner module

BLRun.scingeRunner.generateInputs(RunnerObj)

Function to generate desired inputs for SCINGE. If the folder/files under RunnerObj.datadir exist, this function will not do anything.

BLRun.scingeRunner.parseOutput(RunnerObj)

Function to parse outputs from SCINGE.

BLRun.scingeRunner.run(RunnerObj)

Function to run SCINGE algorithm

BLRun.scnsRunner module

BLRun.scnsRunner.generateInputs(RunnerObj)

Function to generate desired inputs for SCNS. If the folder/files under RunnerObj.datadir exist, this function will not do anything.

BLRun.scnsRunner.parseOutput(RunnerObj)

Function to parse output from SCNS

BLRun.scnsRunner.run(RunnerObj)

Function to run SCNS algorithm

BLRun.scodeRunner module

BLRun.scodeRunner.generateInputs(RunnerObj)

Function to generate desired inputs for SCODE. If the folder/files under RunnerObj.datadir exist, this function will not do anything.

BLRun.scodeRunner.parseOutput(RunnerObj)

Function to parse outputs from SCODE.

BLRun.scodeRunner.run(RunnerObj)

Function to run SCODE algorithm

BLRun.scribeRunner module

BLRun.scribeRunner.generateInputs(RunnerObj)

Function to generate desired inputs for SCRIBE. If the folder/files under RunnerObj.datadir exist, this function will not do anything.

BLRun.scribeRunner.parseOutput(RunnerObj)

Function to parse outputs from SCRIBE.

BLRun.scribeRunner.run(RunnerObj)

Function to run SCRIBE algorithm. To see all the inputs runScribe.R script takes, run: docker run scribe:base /bin/sh -c “Rscript runScribe.R -h”

BLRun.sinceritiesRunner module

BLRun.sinceritiesRunner.generateInputs(RunnerObj)

Function to generate desired inputs for SINCERITIES. If the folder/files under RunnerObj.datadir exist, this function will not do anything.

Parameters:RunnerObj – An instance of the BLRun

BLRun.sinceritiesRunner.parseOutput(RunnerObj)

Function to parse outputs from SINCERITIES.

Parameters:RunnerObj – An instance of the BLRun

BLRun.sinceritiesRunner.run(RunnerObj)

Function to run SINCERITIES algorithm

Parameters:RunnerObj – A BLRun object