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P

P_VAL_CUTOFF - Static variable in class biolockj.module.report.r.R_Module

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"

PARAMS - Static variable in class biolockj.Constants

Config property suffix for exe.* properties, used to set optional parameters: "Params"

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.

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.
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.
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.

PASSWORD_FLAG - Static variable in class biolockj.util.RuntimeParamUtil

Change password runtime parameter switch: "p"

PathwayUtil - Class in biolockj.util

This utility helps work HumanN2 pathway abundance data.

PDF_EXT - Static variable in class biolockj.Constants

BioLockJ PDF file extension constant: ".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 set to copy input files into pipeline root directory: "pipeline.copyInput"

PIPELINE_DEFAULT_PROPS - Static variable in class biolockj.Constants

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

PIPELINE_DELETE_TEMP_FILES - Static variable in class biolockj.Constants

Config property set to delete BioModule.getTempDir() files: "pipeline.deleteTempFiles"

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 Boolean property: "pipeline.env"
Options: "cluster", "aws", "local"

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_HUMANN2_COUNT_TABLE_INPUT_TYPE - Static variable in class biolockj.util.BioLockJUtil

Pipeline input file type indicating the file is Humann2 generated

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_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_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_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).

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

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

pipelineInputDir() - Static method in class biolockj.BioLockJ

Return the pipeline input directory

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

Convenience method to check pipeline input file type.

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)

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

Return TRUE if pipeline input files are sequence files.

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.

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

Print collection one item per line.

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

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

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.SubProcess - Class in biolockj

Class used to submit processes on their own Thread.

PROJECT_DESC - Static variable in class biolockj.Constants

Config property to assign a free-hand to a project: "project.desc" 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.

PROJECT_PERMISSIONS - Static variable in class biolockj.Constants

Config property to define permission settings when running chmod on pipeline root dir: "pipeline.permissions"

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

PropUtil - Class in biolockj.util

Simple utility containing String manipulation and formatting functions.

PropUtil() - Constructor for class biolockj.util.PropUtil

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

Save EFS data to S3 based on pipeline Config.

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