biolockj.module.classifier

Interface ClassifierModule

All Superinterfaces:

BioModule, ScriptModule, SeqModule

All Known Implementing Classes:

ClassifierModuleImpl, Humann2Classifier, Kraken2Classifier, KrakenClassifier, Metaphlan2Classifier, QiimeClassifier, QiimeClosedRefClassifier, QiimeDeNovoClassifier, QiimeOpenRefClassifier, RdpClassifier

public interface ClassifierModule
extends SeqModule

Classifier BioModules build one or more bash scripts to call the application on sequence files. Contains methods to build bash scripts for taxonomic assignment of paired and unpaired reads. Contains methods to get classifier command (loaded module, executable file path, or in the $USER $PATH) and optional command line parameters.}

Field Summary

Fields inherited from interface biolockj.module.ScriptModule

SCRIPT_BATCH_SIZE, SCRIPT_DEFAULT_HEADER, SCRIPT_NUM_THREADS, SCRIPT_PERMISSIONS, SCRIPT_TIMEOUT

Fields inherited from interface biolockj.module.BioModule

MAIN_SCRIPT_PREFIX, OUTPUT_DIR, TEMP_DIR

Method Summary

Modifier and Type	Method and Description
String	getClassifierExe() Get the executable required to classify your samples.
List<String>	getClassifierParams() Get optional list of parameters to append whenever the classifier executable is called.

Methods inherited from interface biolockj.module.SeqModule

getSeqFiles

Methods inherited from interface biolockj.module.ScriptModule

buildScript, buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout, getWorkerScriptFunctions

Methods inherited from interface biolockj.module.BioModule

checkDependencies, cleanUp, executeTask, getID, getInputFiles, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getSummary, getTempDir, init, isValidInputModule

Method Detail

getClassifierExe

String getClassifierExe()
                 throws Exception

Get the executable required to classify your samples.

Returns:

Command to execute classifier program

Throws:

Exception - if the classifier program undefined or invalid

getClassifierParams

List<String> getClassifierParams()
                          throws Exception

Get optional list of parameters to append whenever the classifier executable is called.

Returns:

Runtime parameters

Throws:

Exception - thrown if parameters defined are invalid