biolockj.module.report.taxa

Class NormalizeTaxaTables

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.NormalizeTaxaTables

All Implemented Interfaces:

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

public class NormalizeTaxaTables
extends TransformTaxaTables
implements ApiModule

This utility is used to normalize and/or log-transform the raw OTU counts using the formulas:

• Normalized OTU count formula = (RC/n)*((SUM(x))/N)+1
• Relative abundance formula = Log(log_base) [ (RC/n)*((SUM(x))/N)+1 ]

The code implementation supports (log_base = e) and (log_base = 10) which is configured via Constants.REPORT_LOG_BASE property.

• RC = Sample OTU count read in from each Sample-OTU cell in the raw count file passed to the constructor
• n = number of sequences in the sample, read in as the row sum (sum of OTU counts for the sample)
• SUM(x) = total number of counts in the table, read in as the table sum (sum of OTU counts for all samples)
• N = total number of samples, rowCount - 1 (header row)

Further explanation regarding the normalization scheme, please read The ISME Journal 2013 paper by Dr. Anthony Fodor: "Stochastic changes over time and not founder effects drive cage effects in microbial community assembly in a mouse model" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3806260/

GUI Module Name

Normalize Taxa Tables

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
NormalizeTaxaTables()

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.
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) Populate normalized counts with the formula: (RC/n)*((SUM(x))/N)+1
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, 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, 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, getPreRequisiteModules, getPropDefault, getResourceDir, getTempDir, init, isValidInputModule, setAlias

Methods inherited from interface biolockj.module.ScriptModule

buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout

Constructor Detail

NormalizeTaxaTables

public NormalizeTaxaTables()

Method Detail

transform

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

Populate normalized counts with the formula: (RC/n)*((SUM(x))/N)+1

Specified by:

transform in class TransformTaxaTables

Parameters:

taxaTable - OTU raw count table

Returns:

A

Throws:

Exception - if unable to construct NormalizeTaxaTables

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

getProcessSuffix

protected String getProcessSuffix()

Specified by:

getProcessSuffix in class TransformTaxaTables

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

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: