biolockj.module.report.taxa

Class TransformTaxaTables

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.JavaModuleImpl

biolockj.module.report.taxa.TaxaCountModule

biolockj.module.report.taxa.TransformTaxaTables

All Implemented Interfaces:

BioModule, JavaModule, ScriptModule, Comparable<BioModule>

Direct Known Subclasses:

AddPseudoCount, LogTransformTaxaTables, NormalizeByReadsPerMillion, NormalizeTaxaTables, ShannonDiversity

public abstract class TransformTaxaTables
extends TaxaCountModule

This utility is used to normalize, log-transform or othewise transfrom data that is stored as taxa counts. This uses the TaxaCountModule methods to get taxa table files, and uses the functionality to writing taxa table data. It is generally assumed that the output will contain the same samples and taxa as the input. If any samples or taxa are removed that should be abundantly clear. The provided filterSamples removes all samples that have all-0 values.

Field Summary

Fields inherited from class biolockj.module.JavaModuleImpl

BLJ_OPTIONS

Fields inherited from class biolockj.module.BioModuleImpl

GZIP_EXT, LOG_EXT, PDF_EXT, RETURN, SH_EXT, TAB_DELIM, TSV_EXT, TXT_EXT

Fields inherited from interface biolockj.module.BioModule

LOG_DIR, MAIN_SCRIPT_PREFIX, NO_VERSION, OUTPUT_DIR, RES_DIR, TEMP_DIR

Constructor Summary

Constructors

Constructor and Description
TransformTaxaTables()

Method Summary

Modifier and Type	Method and Description
protected List<String>	filterSamples(TaxaLevelTable inputData) Filter out any samples in which all values are 0.
protected List<String>	filterTaxa(TaxaLevelTable inputData)
protected File	getOutputFile(File inputFile)
protected abstract String	getProcessSuffix()
void	runModule() This method executes the modules primary Java routine.
protected abstract TaxaLevelTable	transform(TaxaLevelTable inputData, List<String> filteredSampleIDs, List<String> filteredTaxaIDs) Transform a table of values.

Methods inherited from class biolockj.module.report.taxa.TaxaCountModule

filterByProcessLevel, getDetails, getInputFiles, getPreRequisiteModules, isTaxaModule, isValidInputModule

Methods inherited from class biolockj.module.JavaModuleImpl

buildScript, executeTask, getDockerImageName, getDockerImageOwner, getDockerImageTag, getWorkerScriptFunctions, markStatus, moduleComplete, moduleFailed, runBioLockJ_CMD

Methods inherited from class biolockj.module.ScriptModuleImpl

buildScriptForPairedReads, checkDependencies, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getSummary, getTimeout, hasScripts, isValidProp

Methods inherited from class biolockj.module.BioModuleImpl

addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getFileCache, getID, getLogDir, getMenuPlacement, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPropDefault, getPropDescMap, getPropType, getPropTypeMap, getResourceDir, getTempDir, getTitle, hashCode, init, listProps, setAlias, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface biolockj.module.ScriptModule

buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout

Methods inherited from interface biolockj.module.BioModule

checkDependencies, cleanUp, getAlias, getID, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPropDefault, getResourceDir, getSummary, getTempDir, init, setAlias, version

Constructor Detail

TransformTaxaTables

public TransformTaxaTables()

Method Detail

runModule

public void runModule()
               throws Exception

Description copied from interface: JavaModule

This method executes the modules primary Java routine.

Specified by:

runModule in interface JavaModule

Specified by:

runModule in class JavaModuleImpl

Throws:

Exception - thrown if any runtime error occurs

transform

protected abstract TaxaLevelTable transform(TaxaLevelTable inputData,
                                            List<String> filteredSampleIDs,
                                            List<String> filteredTaxaIDs)
                                     throws Exception

Transform a table of values. The transform method may or may not make use of the values that were filtered out.

Parameters:

inputData - the data to be transformed without filtering

filteredSampleIDs - Sample ids after filtering

filteredTaxaIDs - Taxa names after filtering

Returns:

A

Throws:

Exception

filterSamples

protected List<String> filterSamples(TaxaLevelTable inputData)

Filter out any samples in which all values are 0.

Parameters:

inputData -

Returns:

filterTaxa

protected List<String> filterTaxa(TaxaLevelTable inputData)

getOutputFile

protected File getOutputFile(File inputFile)
                      throws Exception

Throws:

Exception

getProcessSuffix

protected abstract String getProcessSuffix()