A B C D E F G H I J K L M N O P Q R S T U V W X Y

P

P_VAL_CUTOFF - Static variable in class biolockj.Constants

Config property "r.pvalCutoff" defines the p-value cutoff for significance

P_VALS_NP - Static variable in class biolockj.module.report.r.R_CalculateStats

Non parametric p-value identifier: "nonParametricPvals"

P_VALS_NP_ADJ - Static variable in class biolockj.module.report.r.R_CalculateStats

Non parametric adjusted p-value identifier: "adjNonParPvals"

P_VALS_PAR - Static variable in class biolockj.module.report.r.R_CalculateStats

Parametric p-value identifier: "parametricPvals"

P_VALS_PAR_ADJ - Static variable in class biolockj.module.report.r.R_CalculateStats

Parametric adjusted p-value identifier: "adjParPvals"

PARAM - Static variable in class biolockj.module.diy.GenMod

Config property: "genMod.param"

parameters - Variable in class biolockj.launch.LaunchProcess

parentTaxaLevel(String) - Static method in class biolockj.util.TaxaUtil

Get parent level name of the given level parameter.

parseCountTable(File) - Static method in class biolockj.util.BioLockJUtil

Read in BioLockJ count table, each inner lists represents 1 line from the file.
Each cell in the tab delimited file is stored as 1 element in the inner lists.

ParsedSample - Class in biolockj.node

ParserModules create and store one ParsedSample, with OTU assignments and counts, for each sample.

ParsedSample(OtuNode) - Constructor for class biolockj.node.ParsedSample

Construct a new ParsedSample with it's 1st OtuNode.

ParserModule - Interface in biolockj.module.implicit.parser

This interface defines the required methods to parse ClassifierModule output.

ParserModuleImpl - Class in biolockj.module.implicit.parser

Parser BioModules read ClassifierModule output to build standardized OTU count tables.

ParserModuleImpl() - Constructor for class biolockj.module.implicit.parser.ParserModuleImpl

parseRow(String, boolean) - Method in class biolockj.module.implicit.ImportMetadata

Method called to parse a row from the metadata file, where Config."metadata.columnDelim" separates columns.

parseSample(File) - Method in class biolockj.module.implicit.parser.wgs.Kraken2Parser

parseSample(File) - Method in class biolockj.module.implicit.parser.wgs.KrakenParser

Construct a new KrakenNode

parseSamples() - Method in interface biolockj.module.implicit.parser.ParserModule

Parse ClassifierModule output to build ParsedSamples.

parseSamples() - Method in class biolockj.module.implicit.parser.ParserModuleImpl

parseSamples() - Method in class biolockj.module.implicit.parser.r16s.QiimeParser

Parse lowest level QiimeClassifier report in the input directory.

parseSamples() - Method in class biolockj.module.implicit.parser.r16s.RdpParser

Parse all RdpClassifier reports in the input directory.
Build an RdpNode for each line.
If RdpParser.isValid(OtuNode),
Create ParsedSample for the OtuNodeImpl.getSampleId() if not yet created.

parseSamples() - Method in class biolockj.module.implicit.parser.wgs.Humann2Parser

To parse the taxonomy level reports output by Humann2Classifier.

parseSamples() - Method in class biolockj.module.implicit.parser.wgs.Kraken2Parser

Parse all Kraken2Classifier reports in the input directory.
Cache the leaf counts Build an Kraken2Node for each line.
If ParserModuleImpl.isValid(OtuNode),
Create ParsedSample for the OtuNodeImpl.getSampleId() if not yet created.

parseSamples() - Method in class biolockj.module.implicit.parser.wgs.KrakenParser

Parse all KrakenClassifier reports in the input directory.
Cache the leaf counts Build an KrakenNode for each line.
If ParserModuleImpl.isValid(OtuNode),
Create ParsedSample for the OtuNodeImpl.getSampleId() if not yet created.

parseSamples() - Method in class biolockj.module.implicit.parser.wgs.Metaphlan2Parser

To parse the taxonomy level reports output by Metaphlan2Classifier: Create ParsedSample for the OtuNodeImpl.getSampleId() if not yet created.

partiallyInitialize(File) - Static method in class biolockj.Config

PASS - Static variable in class biolockj.util.ValidationUtil

passEnvironmentVarVals(ScriptModule) - Static method in class biolockj.util.BashScriptBuilder

PASSWORD - Static variable in class biolockj.util.RuntimeParamUtil

Change password runtime parameter switch: "-password"

PASSWORD_ARG - Static variable in class biolockj.launch.LaunchProcess

PathMapper - Interface in biolockj.util.paths

pathVariableVals(ScriptModule) - Static method in class biolockj.util.BashScriptBuilder

Get the script lines to assign values to the common directories.

PathwayUtil - Class in biolockj.util

This utility helps work HumanN2 pathway abundance data.

pauseToRead() - Static method in class biolockj.launch.Launcher

PDF_EXT - Static variable in class biolockj.Constants

BioLockJ PDF file extension: ".pdf"

PDF_EXT - Static variable in class biolockj.module.BioModuleImpl

BioLockJ PDF file extension constant: ".pdf"

PearMergeReads - Class in biolockj.module.seq

This BioModule will merge forward and reverse fastq files using PEAR.
For more informations, see the online PEAR manual: https://sco.h-its.org/exelixis/web/software/pear/doc.html

PearMergeReads() - Constructor for class biolockj.module.seq.PearMergeReads

PHYLUM - Static variable in class biolockj.Constants

Config option for "report.taxonomyLevels": "phylum"

PHYLUM_DELIM - Static variable in class biolockj.node.OtuNodeImpl

Standard classifier output level delimiter for PHYLUM

PICK_OTU_SCRIPT - Static variable in class biolockj.module.classifier.r16s.QiimeClosedRefClassifier

Closed reference OTU picking script: "pick_closed_reference_otus.py"

PICK_OTU_SCRIPT - Static variable in class biolockj.module.classifier.r16s.QiimeDeNovoClassifier

De novo OTU picking script: "pick_de_novo_otus.py"

PICK_OTU_SCRIPT - Static variable in class biolockj.module.classifier.r16s.QiimeOpenRefClassifier

Open reference OTU picking script: "pick_open_reference_otus.py"

Pipeline - Class in biolockj

This class initializes and executes each BioModule configured for execution.
BioModules that generate scripts are monitored until all scripts are complete, before moving on to the next module.

PIPELINE_COPY_FILES - Static variable in class biolockj.Constants

Config property: "pipeline.copyInput"

PIPELINE_DEFAULT_PROPS - Static variable in class biolockj.Constants

Config String property: "pipeline.defaultProps"

PIPELINE_DESC - Static variable in class biolockj.Constants

Config property to allow a free-hand description to a pipeline: "pipeline.desc" TODO: needs to be implemented.

PIPELINE_ENV - Static variable in class biolockj.Constants

Config String property: "pipeline.env"

PIPELINE_ENV_AWS - Static variable in class biolockj.Constants

Config option for property: "pipeline.env"
Used to indicate running as an Amazon web service: "aws"

PIPELINE_ENV_CLUSTER - Static variable in class biolockj.Constants

Config option for property: "pipeline.env"
Used to indicate running on the cluster: "cluster"

PIPELINE_ENV_LOCAL - Static variable in class biolockj.Constants

Config option for property: "pipeline.env"
Used to indicate running on a local machine (laptop, etc): "local"

PIPELINE_ENV_VARS - Static variable in class biolockj.Constants

Config List property: "pipeline.env"

PIPELINE_ENV_VARS_DESC - Static variable in class biolockj.Constants

PIPELINE_HUMANN2_COUNT_TABLE_INPUT_TYPE - Static variable in class biolockj.util.BioLockJUtil

Pipeline input file type indicating the file is Humann2 generated

PIPELINE_LOCATION_KEY - Static variable in class biolockj.Constants

Indicator for related programs (bash code, sheepdog_testing_suite) of the pipelines path: "Pipeline root directory: "

PIPELINE_LOG_NORMAL_TAXA_COUNT_TABLE_INPUT_TYPE - Static variable in class biolockj.util.BioLockJUtil

Internal Config String property: "taxa_count_log_norm"
Set as the value of "internal.pipelineInputTypes" for log-normalized taxa count files that meet the file requirements to pass TaxaUtil.isLogNormalizedTaxaFile(File).

PIPELINE_NAME - Static variable in class biolockj.Constants

Config property to assign a name to a pipeline: "pipeline.name" TODO: needs to be implemented.

PIPELINE_NORMAL_TAXA_COUNT_TABLE_INPUT_TYPE - Static variable in class biolockj.util.BioLockJUtil

Internal Config String property: "taxa_count_norm"
Set as the value of "internal.pipelineInputTypes" for normalized taxa count files that meet the file requirements to pass TaxaUtil.isNormalizedTaxaFile(File).

PIPELINE_OTU_COUNT_TABLE_INPUT_TYPE - Static variable in class biolockj.util.BioLockJUtil

Internal Config String property: "otu_count"
Set as the value of "internal.pipelineInputTypes" for OTU count files that meet the file requirements to pass OtuUtil.isOtuFile(File).

PIPELINE_PAIRED_READS_INPUT_TYPE - Static variable in class biolockj.util.BioLockJUtil

Internal Config String property: "paired"
Set as the value of "internal.pipelineInputTypes" for paired sequence input files.

PIPELINE_PARSER_INPUT_TYPE - Static variable in class biolockj.util.BioLockJUtil

Internal Config String property: "classifier_output"
Set as the value of "internal.pipelineInputTypes" for classifier output files.

PIPELINE_PRIVS - Static variable in class biolockj.Constants

Config property: "pipeline.permissions"

PIPELINE_R_INPUT_TYPE - Static variable in class biolockj.util.BioLockJUtil

Internal Config String property: "R"
Set as the value of "internal.pipelineInputTypes" if input files are some type of count table merged with the metadata such as those output by AddMetadataToTaxaTables.

PIPELINE_SEQ_INPUT_TYPE - Static variable in class biolockj.util.BioLockJUtil

Internal Config String property: "seq"
Set as the value of "internal.pipelineInputTypes" for sequence input files.

PIPELINE_STATS_TABLE_INPUT_TYPE - Static variable in class biolockj.util.BioLockJUtil

Internal Config String property: "stats"
Set as the value of "internal.pipelineInputTypes" if input files are tables of statistics such as those output by R_CalculateStats.

PIPELINE_STATUS - Static variable in class biolockj.util.SummaryUtil

PIPELINE_TAXA_COUNT_TABLE_INPUT_TYPE - Static variable in class biolockj.util.BioLockJUtil

Internal Config String property: "taxa_count"
Set as the value of "internal.pipelineInputTypes" for taxa count files that meet the file requirements to pass TaxaUtil.isTaxaFile(File).

PIPELINE_USE_EVARS - Static variable in class biolockj.Constants

Config List property: "pipeline.useEnvVars"
"when evaluating variables in the ${VAR} format, should environment variables be used. Regardless, priority is given to variable values defined in the config file."

PIPELINE_USE_EVARS_DESC - Static variable in class biolockj.Constants

PipelineFormationException - Exception in biolockj.exception

PipelineFormationException is thrown when there is a problem in setting up the modules to run.

PipelineFormationException(String) - Constructor for exception biolockj.exception.PipelineFormationException

pipelineInputContainsOtuSummary() - Static method in class biolockj.module.report.JsonReport

Check pipeline input to see if OTU summary file is the only pipeline input file.

pipelineInputType(String) - Static method in class biolockj.util.BioLockJUtil

Convenience method to check pipeline input file type.

pipelineInternalInputDir() - Static method in class biolockj.util.BioLockJUtil

Return the pipeline input directory

pipelineName() - Static method in class biolockj.Config

Get the current pipeline name (root folder name)

pipelinePath() - Static method in class biolockj.Config

Get the current pipeline absolute directory path (root folder path)

PipelineScriptException - Exception in biolockj.exception

PipelineScriptException is thrown by BashScriptBuilder if errors occur writing MASTER & WORKER scripts.

PipelineScriptException(ScriptModule, boolean, String) - Constructor for exception biolockj.exception.PipelineScriptException

Create standard error to throw writing MASTER & WORKER bash scripts.

PipelineScriptException(ScriptModule, String) - Constructor for exception biolockj.exception.PipelineScriptException

Create standard error to throw if problems occur generating pipeline bash scripts.

PipelineScriptException(String) - Constructor for exception biolockj.exception.PipelineScriptException

Create a standard exception message.

PipelineUtil - Class in biolockj.pipelines

PipelineUtil() - Constructor for class biolockj.pipelines.PipelineUtil

piplineHasSeqInput() - Static method in class biolockj.util.SeqUtil

Return TRUE if pipeline input files are sequence files.

PLS_USE_INSTALL - Static variable in class biolockj.launch.LaunchProcess

poll(ScriptModule) - Static method in class biolockj.Pipeline

The ScriptModule.getScriptDir() will contain one main script and one ore more worker scripts.
An empty file with appended to the script name is created when execution begins.
If successful, an empty file with appended to the script name is created.
Upon failure, an empty file with appended to the script name is created.
Script status is polled each minute, determining status by counting indicator files.
Log outputs the # of started, failed, and successful scripts (if any change).
Log repeats the previous message every 10 minutes if no status change is detected.

populateInBetweenTaxa() - Method in class biolockj.node.OtuNodeImpl

Populate missing OTUs if top level taxa is defined and there is a level gap between the top level and the bottom level.

POS_INTEGER_TYPE - Static variable in class biolockj.Properties

PRECHECK_ARG - Static variable in class biolockj.launch.LaunchProcess

PRECHECK_COMPLETE - Static variable in class biolockj.Constants

Name of the file created in the BioModule root directory to indicate the precheck process encountered an error (if running in precheck mode): "precheckComplete"

PRECHECK_FAILED - Static variable in class biolockj.Constants

Name of the file created in the BioModule root directory to indicate the precheck process has completed (if running in precheck mode): "precheckFailed"

PRECHECK_FLAG - Static variable in class biolockj.util.RuntimeParamUtil

Flag argument; if present, BioLockJ will stop after checkDependencies step.

PRECHECK_STARTED - Static variable in class biolockj.Constants

Name of the file created in the BioModule root directory to indicate the precheck process has started (if running in precheck mode): "precheckStarted"

printActionOptions() - Method in class biolockj.launch.LaunchProcess

printArgsDescriptions() - Static method in class biolockj.util.RuntimeParamUtil

Print arg descriptions TODO: PROBLEMATIC APPROACH TO SHOW ARGS BY PRINTING VARIABLES IN THIS METHOD

printHelp() - Static method in class biolockj.launch.LaunchProcess

Print the help to standard err.

printHelp(PrintStream) - Static method in class biolockj.launch.LaunchProcess

Print the help menu.

printInfo() - Method in class biolockj.launch.LaunchProcess

printLongFormList(Collection<?>) - Static method in class biolockj.util.BioLockJUtil

Print collection one item per line.

printPipeDir() - Method in class biolockj.launch.LaunchProcess

Print the path to the pipeline root to standard out.

printPipelineStatus(int) - Method in class biolockj.launch.LaunchProcess

Show the status the just-launched pipeline.

printRuntimeArgs(String[]) - Static method in class biolockj.util.RuntimeParamUtil

Print the runtime args to System.out or using the Logger based on useSysOut parameter.

printStatus(String, boolean) - Static method in class biolockj.launch.ProgressUtil

Print a message to the screen.

printVersion() - Static method in class biolockj.launch.LaunchProcess

Print the version to standard out.

PROCESSED - Static variable in class biolockj.Constants

File suffix appended to processed samples in the module output directory: "_reported.tsv"

Processor - Class in biolockj

ScriptModules that generate scripts will submit a main script to the OS for execution as a Processor.

Processor() - Constructor for class biolockj.Processor

Empty constructor to facilitate subprocess creation

Processor.Subprocess - Class in biolockj

Class used to submit processes on their own Thread.

ProgressMsgDemo - Class in biolockj.launch

ProgressMsgDemo() - Constructor for class biolockj.launch.ProgressMsgDemo

ProgressUtil - Class in biolockj.launch

This utility controls the information printed to the screen during launch.

ProgressUtil() - Constructor for class biolockj.launch.ProgressUtil

Utility class, no instantiation.

PROJ_ARG - Static variable in class biolockj.launch.LaunchProcess

PROJECT_DEFAULT_PROPS - Static variable in class biolockj.Constants

Config String property: "project.defaultProps"
Set file path of default property file.

PROJECT_DESC - Static variable in class biolockj.Constants

Config property to assign a free-hand to a project: "project.description" TODO: needs to be implemented.

PROJECT_NAME - Static variable in class biolockj.Constants

Config property to assign a name to a project: "project.name" TODO: needs to be implemented.

promptChange() - Static method in exception biolockj.exception.ConfigException

propDescModule(String, String) - Static method in class biolockj.api.BioLockJ_API

Properties - Class in biolockj

Load properties defined in the BioLockJ configuration file, including inherited properties from project.defaultProps

Properties() - Constructor for class biolockj.Properties

Default constructor.

Properties(Properties) - Constructor for class biolockj.Properties

Constructor called when "pipeline.defaultProps" contains a valid file-path

propInfo() - Static method in class biolockj.api.BioLockJ_API

For each of the properties registered to the Properties class, report the property name, type, description and default value.

props - Static variable in class biolockj.Config

PROPS_EXT - Static variable in class biolockj.Constants

BioLockJ properties file extension: ".properties"

propTypeModule(String, String) - Static method in class biolockj.api.BioLockJ_API

Returns a string describing the format type that required for the value of the property given.

propValue(String, String, BioModule) - Static method in class biolockj.api.BioLockJ_API

Returns the value for that property (first String) If a second argument is given, it is assumed to be the primary config file.

propValue(String, BioModule) - Static method in class biolockj.api.BioLockJ_API

propValue(String) - Static method in class biolockj.api.BioLockJ_API

PURE_DOCKER_PIPELINE_DIR - Static variable in class biolockj.util.DockerUtil

When running in pure docker to do the initial setup, use this pipelines dir: "/workspace/pipelines"

purgeEfsData() - Static method in class biolockj.util.NextflowUtil

Purge EFS data based on pipeline Config.

A B C D E F G H I J K L M N O P Q R S T U V W X Y