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

B

BARCODE_CUTOFF - Static variable in class biolockj.util.DemuxUtil

Config boolean property "demultiplexer.barcodeCutoff" will look for barcodes in "metadata.barcodeColumn" to exist in this percentage of multiplex file.

BARCODE_USE_REV_COMP - Static variable in class biolockj.util.DemuxUtil

Config boolean property "demultiplexer.barcodeRevComp" will use the reverse compliment of "metadata.barcodeColumn" to match sample IDs to sequences.

barcodeInHeader() - Static method in class biolockj.util.DemuxUtil

Return TRUE if Config is setup to demultiplex the sequence data based on bar-codes in the sequence headers.

barcodeInMapping() - Static method in class biolockj.util.DemuxUtil

Return TRUE if Config is setup to demultiplex the sequence data based on bar-codes in the sequence itself.

barcodeInSeq() - Static method in class biolockj.util.DemuxUtil

Return TRUE if Config is setup to demultiplex the sequence data based on bar-codes in the sequence itself.

BASE_DIR_FLAG - Static variable in class biolockj.util.RuntimeParamUtil

Pipeline parent directory file-path runtime parameter switch: "b"

BashScriptBuilder - Class in biolockj.util

This utility class generates the bash script files using the lines provided and Config script properties.

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

Name of each batch mapping file (each in its own batch directory)

BINARY_FIELDS - Static variable in class biolockj.util.RMetaUtil

Config Internal List property: "R_internal.binaryFields"
Binary fields contain only 2 unique non-NA options

biolockj - package biolockj

The root biolockj package contains core classes used by all BioLockJ pipelines.

BioLockJ - Class in biolockj

This is the primary BioLockJ class - its main() method is executed when the jar is run.
This class validates the runtime parameters to run a new pipeline or restart a failed pipeline.
The Java log file is initialized and the configuration file is processed before starting the pipeline.
If the pipeline is successful, the program executes clean up operations (if configured) and creates a status-complete indicator file in the pipeline root directory.

biolockj.exception - package biolockj.exception

This package contains Exception subclasses specific to BioLockJ.

biolockj.module - package biolockj.module

Pipeline modules are loaded based on the BioModules listed in the Config file.
All modules (i.e., implement BioModule) are contained within this package or its sub-packages.

biolockj.module.classifier - package biolockj.module.classifier

This package contains Classifier specific BioModules that build bash scripts to generate taxonomy reports from the sequences files.

biolockj.module.classifier.r16s - package biolockj.module.classifier.r16s

This package contains RDP and QIIME classifier modules that assign taxonomy to 16s sequences.
Output file formats are classifier specific so classifier requires a unique post-requisite ParserModule.

biolockj.module.classifier.wgs - package biolockj.module.classifier.wgs

This package contains Kraken, Kraken2, Humann2, MetaPhlAn classifier modules that assign taxonomy to WGS data.
As with all BioLockJ classifiers, these modules generate raw classifier output files from the sequence data.
Include the corresponding ParserModule in the Config file to generate standardized OTU abundance tables.

biolockj.module.implicit - package biolockj.module.implicit

The modules in this package are implicitly added to pipelines as needed.
These modules cannot be directly added to any pipeline unless overridden via pipeline.disableImplicitModules=Y.

biolockj.module.implicit.parser - package biolockj.module.implicit.parser

This package contains Parser BioModules in the r16s and WGS sub-packages that are paired with a ClassifierModule via BioModule.getPostRequisiteModules() to run immediately after the classifier.

biolockj.module.implicit.parser.r16s - package biolockj.module.implicit.parser.r16s

This package contains Parser BioModules that convert the 16S taxonomy reports generated by 16S classifiers (such as RDP and QIIME) into standardized OTU abundance tables.

biolockj.module.implicit.parser.wgs - package biolockj.module.implicit.parser.wgs

This package contains Parser BioModules that convert the WGS taxonomy reports generated by WGS classifiers (such as Kraken, Kraken2 Metaphlan2, or Humann2) into standardized OTU abundance tables.

biolockj.module.implicit.qiime - package biolockj.module.implicit.qiime

This package contains BioModules that are implicitly added to QIIME pipeline as needed.

biolockj.module.report - package biolockj.module.report

This package contains BioModules that normalize OTU abundance tables output by Parser modules, merges them with the metadata, and generates various reports and notifications.

biolockj.module.report.humann2 - package biolockj.module.report.humann2

biolockj.module.report.otu - package biolockj.module.report.otu

biolockj.module.report.r - package biolockj.module.report.r

This package contains BioModules that build pipeline reports from the standard OTU abundance tables by generating R scripts to produce the summary statistics and data visualizations output to PDF files.

biolockj.module.report.taxa - package biolockj.module.report.taxa

biolockj.module.seq - package biolockj.module.seq

BioModules used to prepare sequence files or update the metadata prior to classification.

biolockj.node - package biolockj.node

Package biolockj.node contains core classes instantiated by the ParserModule to hold Sample ID-(OTU name/count) data read in from ClassifierModule output.

biolockj.node.r16s - package biolockj.node.r16s

Package contains RDP and QIIME specific OtuNodes that represent the OTUs (operational taxonomy units) assigned by 16S ClassifierModules

biolockj.node.wgs - package biolockj.node.wgs

Package contains Kraken, Kraken2, and MetaPhlAn2 specific OtuNodes that represent the OTUs (operational taxonomy units) assigned by WGS ClassifierModules

biolockj.util - package biolockj.util

Static utilities centralize and organize reusable core methods.

BioLockJUtil - Class in biolockj.util

Simple utility containing String manipulation and formatting functions.

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

BioModule - Interface in biolockj.module

Classes that implement this interface are eligible to be included in a BioLockJ pipeline.
Use the #BioModule tag with the class name in the Config file to include a module.
The Pipeline class executes BioModules in the order provided in the Config file.

BioModuleFactory - Class in biolockj

This class initializes pipeline modules, starting with those in the Config file and adding the prerequisite and post-requisite modules.

BioModuleImpl - Class in biolockj.module

Superclass for standard BioModules (classifiers, parsers, etc).

BioModuleImpl() - Constructor for class biolockj.module.BioModuleImpl

BLJ_BASH - Static variable in class biolockj.util.DockerUtil

Docker image name for simple bash scripts (awk,gzip,pear).

BLJ_COMPLETE - Static variable in class biolockj.Constants

Name of the file created in the BioModule or "internal.pipelineDir" root directory to indicate execution was successful: "biolockjComplete"

BLJ_FAILED - Static variable in class biolockj.Constants

Name of the file created in the "internal.pipelineDir" root directory to indicate fatal application errors halted execution: "biolockjFailed"

BLJ_MODULE_TAG - Static variable in class biolockj.Constants

Set "#BioModule" tag in Config file to include in pipeline: "#BioModule"
Example: #BioModule biolockj.module.ImportMetadata

BLJ_OPTIONS - Static variable in class biolockj.module.JavaModuleImpl

Docker environment variable holding the Docker program switches: "BLJ_OPTIONS"

BLJ_STARTED - Static variable in class biolockj.Constants

Name of the file created in the BioModule root directory to indicate execution has started: "biolockjStarted"

BLJ_WIKI - Static variable in class biolockj.Constants

URL to the BioLockJ WIKI

bottomTaxaLevel() - Static method in class biolockj.util.TaxaUtil

Return the bottom configured taxonomy level from Config."report.taxonomyLevels"

breakUpFiles() - Method in class biolockj.module.implicit.Demultiplexer

Some multiplexed files can be very large.

buildConfig(File) - Static method in class biolockj.Properties

Recursive method handles nested default Config files.

buildDockerBashScript() - Method in class biolockj.module.report.r.R_Module

Run R script in docker.

buildDownloadList(Collection<File>) - Static method in class biolockj.util.DownloadUtil

Add files to "downloadList.txt" in pipeline root directory.

buildExecuteFunction(String) - Static method in class biolockj.util.BashScriptBuilder

Create bash worker script function: "execute".
Failure details written to the failure script file if any occur.

buildJsonMap(JsonNode) - Method in class biolockj.module.report.JsonReport

Build JsonMap from the CompileOtuCounts output directory.

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

Build the MIAN script.

buildMessage(String, String) - Static method in exception biolockj.exception.ConfigException

Build a standard error message for Configuration file errors.

buildNewMetadataFile() - Method in class biolockj.module.implicit.ImportMetadata

Create a simple metadata file in the module output directory, with only the 1st column populated with Sample IDs.

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

After ParserModule.parseSamples() completes, this method builds the OTU count files.

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

buildOtuTaxa(String, String) - Static method in class biolockj.util.OtuUtil

Build taxa name into OTU path, returns: level + "__" + taxa

buildPipeline() - Static method in class biolockj.BioModuleFactory

Build all modules for the pipeline.

buildQiimeDockerConfigLines() - Method in class biolockj.module.implicit.qiime.QiimeClassifier

Build ~/.qiime_config to define the alternate Docker qiime_classifier DB with local container path references.

BuildQiimeMapping - Class in biolockj.module.implicit.qiime

This BioModule converts the metadata file into a tab delimited QIIME mapping file (if provided).
The QIIME mapping file is validated by calling QIIME script validate_mapping_file.py

BuildQiimeMapping() - Constructor for class biolockj.module.implicit.qiime.BuildQiimeMapping

buildRarefiedFile(File, List<Long>) - Method in class biolockj.module.seq.RarefySeqs

Build the rarefied file for the input file, keeping only the given indexes

buildRdpNode(String, String) - Method in class biolockj.node.r16s.RdpNode

Build the OtuNode by extracting the OTU names for each level from the line.

buildScript(List<File>) - Method in class biolockj.module.classifier.r16s.QiimeClosedRefClassifier

Create bash script lines to split up the QIIME mapping and fasta files into batches of size Config."script.batchSize"

buildScript(List<File>) - Method in class biolockj.module.classifier.r16s.QiimeDeNovoClassifier

Return bash script lines to pick de novo OTUs by calling QiimeClassifier getPickOtuLines() method.

buildScript(List<File>) - Method in class biolockj.module.classifier.r16s.QiimeOpenRefClassifier

Return bash script lines to pick open reference OTUs by passing the newest biom file in the temp directory [via bash code "$(ls -t $tempDir/*.biom | head -1)"] to QiimeClassifier getPickOtuLines() method.

buildScript(List<File>) - Method in class biolockj.module.classifier.r16s.RdpClassifier

Build bash script lines to classify unpaired reads with RDP.

buildScript(List<File>) - Method in class biolockj.module.classifier.wgs.Humann2Classifier

buildScript(List<File>) - Method in class biolockj.module.classifier.wgs.Kraken2Classifier

Build bash script lines to classify unpaired WGS reads with Kraken2.

buildScript(List<File>) - Method in class biolockj.module.classifier.wgs.KrakenClassifier

Build bash script lines to classify unpaired WGS reads with Kraken.

buildScript(List<File>) - Method in class biolockj.module.classifier.wgs.Metaphlan2Classifier

Build bash script lines to classify unpaired WGS reads with Metaphlan.

buildScript(List<File>) - Method in class biolockj.module.implicit.qiime.BuildQiimeMapping

Create the Qiime corrected mapping file by building a new metadata file with ordered columns, and verify the format via the "validate_mapping_file.py" script.

buildScript(List<File>) - Method in class biolockj.module.implicit.qiime.MergeQiimeOtuTables

Build a single bash script line to call "merge_otu_tables.py" to create the single "otu_table.biom", as required by QiimeParser.

buildScript(List<File>) - Method in class biolockj.module.implicit.qiime.QiimeClassifier

Generate bash script lines to summarize QIIME results, build taxonomy reports, and add alpha diversity metrics.

buildScript(List<File>) - Method in class biolockj.module.JavaModuleImpl

Java script only require 2 lines, one to run the blj_config to update our $PATH and gain access to environment variables, and then the direct call to the BioLockJ.jar.

buildScript(List<File>) - Method in class biolockj.module.report.r.R_Module

Not needed for R script modules.

buildScript(List<File>) - Method in interface biolockj.module.ScriptModule

Method returns a nested list of bash script lines to classify samples containing forward reads only.

buildScript(List<File>) - Method in class biolockj.module.ScriptModuleImpl

buildScript(List<File>) - Method in class biolockj.module.seq.AwkFastaConverter

buildScript(List<File>) - Method in class biolockj.module.seq.Gunzipper

buildScript(List<File>) - Method in class biolockj.module.seq.KneadData

buildScript(List<File>) - Method in class biolockj.module.seq.PearMergeReads

Build the script lines for each sample as a nested list.

buildScriptForPairedReads(List<File>) - Method in class biolockj.module.classifier.wgs.Humann2Classifier

buildScriptForPairedReads(List<File>) - Method in class biolockj.module.classifier.wgs.Kraken2Classifier

Build bash script lines to classify paired WGS reads with Kraken.

buildScriptForPairedReads(List<File>) - Method in class biolockj.module.classifier.wgs.KrakenClassifier

Build bash script lines to classify paired WGS reads with Kraken.

buildScriptForPairedReads(List<File>) - Method in class biolockj.module.classifier.wgs.Metaphlan2Classifier

Build bash script lines to classify paired WGS reads with Metaphlan.

buildScriptForPairedReads(List<File>) - Method in class biolockj.module.implicit.qiime.QiimeClassifier

QIIME does not support paired reads

buildScriptForPairedReads(List<File>) - Method in interface biolockj.module.ScriptModule

Method returns a nested list of bash script lines to classify samples containing paired reads.
The inner list contains the bash script lines required to classify 1 sample.

buildScriptForPairedReads(List<File>) - Method in class biolockj.module.ScriptModuleImpl

The default behavior is the same for paired or unpaired data.

buildScriptLinesToMoveValidSeqsToOutputDir(String) - Method in class biolockj.module.seq.KneadData

Move 1 file named /"Sample_ID.fastq/" if module input consists of forward reads only.
If module input contains paired reads, move 2 files named /"Sample_ID_paired_1.fastq/" and /"Sample_ID_paired_2.fastq/" to the module output directory (after renaming them to BioLockJ standards).

buildScripts(ScriptModule, List<List<String>>) - Static method in class biolockj.util.BashScriptBuilder

This method builds the bash scripts required for the given module.
Standard local/cluster pipelines include: 1 MAIN script, 1+ worker-scripts.
Docker R_Modules include: 1 MAIN scirpt, 0 worker-scripts - MAIN.R run by MAIN.sh
Docker *non-R_Modules* include: 1 MAIN scirpt, 1+ worker-scripts - MAIN.sh runs workers
AWS Docker R_Modules include: 0 MAIN scirpts, 0 worker-scripts - MAIN.R run by nextflow
AWS Docker *non-R_Modules* include: 0 MAIN scirpts, 1+ worker-scripts MAIN.sh runs workers

buildSpawnDockerContainerFunction(BioModule) - Static method in class biolockj.util.DockerUtil

Build the "spawnDockerContainer" method, which takes container name, in/out port, and optionally script path parameters.

buildSummaryOtuCountFile(TreeMap<String, Long>) - Method in class biolockj.module.report.otu.CompileOtuCounts

Build Summary OTU count file for all samples.

BuildTaxaTables - Class in biolockj.module.report.taxa

Many R BioModules expect separate tables containing log-normalized taxa counts for each taxonomy level.

BuildTaxaTables() - Constructor for class biolockj.module.report.taxa.BuildTaxaTables

buildTaxonomyTables(TreeMap<String, TreeMap<String, Long>>) - Method in class biolockj.module.report.taxa.BuildTaxaTables

Build taxonomy tables from the sampleTaxaCounts.

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

Build the name of an unclassified taxa using the given "taxa" parameter.
Returns a name like Unclassified (taxa name) Taxa

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