biolockj.module.report.taxa

Class NormalizeByReadsPerMillion

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.JavaModuleImpl

biolockj.module.report.taxa.TaxaCountModule

biolockj.module.report.taxa.TransformTaxaTables

biolockj.module.report.taxa.NormalizeByReadsPerMillion

All Implemented Interfaces:

ApiModule, BioModule, JavaModule, ScriptModule, Comparable<BioModule>

public class NormalizeByReadsPerMillion
extends TransformTaxaTables
implements ApiModule

Normalize each sample for sequencing depth by reporting each value as the number of counts per million counts in a given sample.

Author:

Ivory

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
NormalizeByReadsPerMillion()

Method Summary

Modifier and Type	Method and Description
String	getCitationString() At a minimum, this should return the name and/or url for the wrapped tool.
String	getDescription() Briefly describe what this module does.
String	getDetails() All child classes from this class have this pre-req.
List<String>	getPostRequisiteModules() By default, no post-requisites are required.
List<String>	getPreRequisiteModules() Require taxonomy table module as prerequisite
protected String	getProcessSuffix()
String	getSummary() Returns summary message to be displayed by Email module so must not contain confidential info.
protected TaxaLevelTable	transform(TaxaLevelTable inputData, List<String> filteredSampleIDs, List<String> filteredTaxaIDs) Transform a table of values.
String	version() Changes to a module class should be accompanied by a increment in version.

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

filterSamples, filterTaxa, getOutputFile, runModule

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

filterByProcessLevel, getInputFiles, 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, 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, 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.api.ApiModule

getDescription, getMenuPlacement, getPropType, getTitle, isValidProp, listProps

Methods inherited from interface biolockj.module.BioModule

checkDependencies, cleanUp, executeTask, getAlias, getDockerImageName, getDockerImageOwner, getDockerImageTag, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, getPropDefault, getResourceDir, getTempDir, init, isValidInputModule, setAlias

Methods inherited from interface biolockj.module.ScriptModule

buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout

Constructor Detail

NormalizeByReadsPerMillion

public NormalizeByReadsPerMillion()

Method Detail

transform

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

Description copied from class: TransformTaxaTables

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

Specified by:

transform in class TransformTaxaTables

Parameters:

inputData - the data to be transformed without filtering

filteredSampleIDs - Sample ids after filtering

filteredTaxaIDs - Taxa names after filtering

Returns:

A

Throws:

Exception

getProcessSuffix

protected String getProcessSuffix()

Specified by:

getProcessSuffix in class TransformTaxaTables

getSummary

public String getSummary()
                  throws Exception

Description copied from class: ScriptModuleImpl

Returns summary message to be displayed by Email module so must not contain confidential info. ModuleUtil provides summary metrics on output files

Specified by:

getSummary in interface BioModule

Overrides:

getSummary in class ScriptModuleImpl

Returns:

Summary of BioModule execution

Throws:

Exception - if any error occurs

getPostRequisiteModules

public List<String> getPostRequisiteModules()
                                     throws Exception

Description copied from class: BioModuleImpl

By default, no post-requisites are required.

Specified by:

getPostRequisiteModules in interface BioModule

Overrides:

getPostRequisiteModules in class BioModuleImpl

Returns:

List of BioModules

Throws:

Exception - if invalid Class names are returned as post-requisites

getPreRequisiteModules

public List<String> getPreRequisiteModules()
                                    throws Exception

Description copied from class: TaxaCountModule

Require taxonomy table module as prerequisite

Specified by:

getPreRequisiteModules in interface BioModule

Overrides:

getPreRequisiteModules in class TaxaCountModule

Returns:

List of BioModule Class Names

Throws:

Exception - if invalid Class names are returned as prerequisites

getDescription

public String getDescription()

Description copied from interface: ApiModule

Briefly describe what this module does. A more detailed description may be returned by getDetails.

Specified by:

getDescription in interface ApiModule

Returns:

getDetails

public String getDetails()
                  throws API_Exception

Description copied from class: TaxaCountModule

All child classes from this class have this pre-req.

Specified by:

getDetails in interface ApiModule

Overrides:

getDetails in class TaxaCountModule

Returns:

Throws:

API_Exception

getCitationString

public String getCitationString()

Description copied from interface: ApiModule

At a minimum, this should return the name and/or url for the wrapped tool. For BioLockJ home-grown modules, it can cite BioLockJ and give the current version. Ideally this will include the version for the wrapped tool. Tool version may require using a stored variable that can be filled in during execution; and the string that is returned pre-execution may not have the version.

Specified by:

getCitationString in interface ApiModule

Returns:

version

public String version()

Description copied from interface: BioModule

Changes to a module class should be accompanied by a increment in version. The is a string and open form, but using the major.minor.patch semantic versioning is recommended.

Specified by:

version in interface BioModule

Returns: