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.NormalizeTaxaTables

All Implemented Interfaces:

BioModule, JavaModule, ScriptModule, Comparable<BioModule>

Direct Known Subclasses:

LogTransformTaxaTables

public class NormalizeTaxaTables
extends TaxaCountModule

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

Modifier and Type	Field and Description
protected static String	LOG_10 Log 10 display string as 1/2 supported values for: "report.logBase"
protected static String	LOG_E Log e display string as 1/2 supported values for: "report.logBase"

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.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

Constructor Summary

Constructors

Constructor and Description
NormalizeTaxaTables()

Method Summary

Modifier and Type	Method and Description
void	checkDependencies() Verify Config."report.logBase" property is valid (if defined) with a value = (e or 10).
protected static List<String>	filterZeroSampleIDs(List<String> sampleIDs, Set<Integer> allZeroIndex) Filter Sample IDs with all zero rows
protected static Set<Integer>	findAllZeroIndex(List<List<Long>> data) Return the table index for rows with all zer count values
protected String	getLogBase() Get the Log base (10 or e)
protected static List<String>	getOtuNames(String header) Parse Taxa names from the given header line.
String	getSummary() Returns summary message to be displayed by Email module so must not contain confidential info.
void	runModule() This method executes the modules primary Java routine.
protected void	transform(File taxaTable) Populate normalized OTU counts with the formula: (RC/n)*((SUM(x))/N)+1
protected static void	writeDataToFile(File inputFile, List<String> sampleNames, List<String> taxaNames, List<List<String>> taxaCounts) Write transformed data to file

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

filterByProcessLevel, getInputFiles, getPreRequisiteModules, isTaxaModule, isValidInputModule

Methods inherited from class biolockj.module.JavaModuleImpl

buildScript, executeTask, getSource, getWorkerScriptFunctions, markStatus, moduleComplete, moduleFailed

Methods inherited from class biolockj.module.ScriptModuleImpl

buildScriptForPairedReads, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getTimeout, hasScripts

Methods inherited from class biolockj.module.BioModuleImpl

cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getFileCache, getID, getModuleDir, getOutputDir, getPostRequisiteModules, getTempDir, init, toString, validateFileNameUnique

Methods inherited from class java.lang.Object

clone, finalize, getClass, hashCode, 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

cleanUp, getID, getModuleDir, getOutputDir, getPostRequisiteModules, getTempDir, init

Field Detail

LOG_10

protected static final String LOG_10

Log 10 display string as 1/2 supported values for: "report.logBase"

See Also:

Constant Field Values

LOG_E

protected static final String LOG_E

Log e display string as 1/2 supported values for: "report.logBase"

See Also:

Constant Field Values

Constructor Detail

NormalizeTaxaTables

public NormalizeTaxaTables()

Method Detail

checkDependencies

public void checkDependencies()
                       throws Exception

Verify Config."report.logBase" property is valid (if defined) with a value = (e or 10).

Specified by:

checkDependencies in interface BioModule

Overrides:

checkDependencies in class ScriptModuleImpl

Throws:

ConfigFormatException - if REPORT_LOG_BASE is not set to a valid option (e or 10)

Exception - thrown if missing or invalid dependencies are found

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

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

getLogBase

protected String getLogBase()

Get the Log base (10 or e)

Returns:

Log base

transform

protected void transform(File taxaTable)
                  throws Exception

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

Parameters:

taxaTable - OTU raw count table

Throws:

Exception - if unable to construct NormalizeTaxaTables

filterZeroSampleIDs

protected static List<String> filterZeroSampleIDs(List<String> sampleIDs,
                                                  Set<Integer> allZeroIndex)

Filter Sample IDs with all zero rows

Parameters:

sampleIDs - List of Sample IDs

allZeroIndex - Table row index for all-zero rows

Returns:

Filtered list of Sample IDs

findAllZeroIndex

protected static Set<Integer> findAllZeroIndex(List<List<Long>> data)

Return the table index for rows with all zer count values

Parameters:

data - List of table rows

Returns:

Set of empty zero-rows

getOtuNames

protected static List<String> getOtuNames(String header)

Parse Taxa names from the given header line.

Parameters:

header - Head line of table

Returns:

List of Taxa

writeDataToFile

protected static void writeDataToFile(File inputFile,
                                      List<String> sampleNames,
                                      List<String> taxaNames,
                                      List<List<String>> taxaCounts)
                               throws Exception

Write transformed data to file

Parameters:

inputFile - Count table

sampleNames - Sample

taxaNames - Taxa names

taxaCounts - Taxa counts

Throws:

Exception - if errors occur