biolockj.module.report.taxa

Class AddMetadataToTaxaTables

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.JavaModuleImpl

biolockj.module.report.taxa.TaxaCountModule

biolockj.module.report.taxa.AddMetadataToTaxaTables

All Implemented Interfaces:

BioModule, JavaModule, ScriptModule, Comparable<BioModule>

public class AddMetadataToTaxaTables
extends TaxaCountModule

This BioModule is used to add metadata columns to the OTU abundance tables.

GUI Module Name

Add Metadata to Taxa Tables

Field Summary

Fields

Modifier and Type	Field and Description
static String	HIT_RATIO Metadata column name for column that stores the calculation for: ParserModuleImpl.getOtuCountField()/ RegisterNumReads.getNumReadFieldName(): "Hit_Ratio".
static String	META_MERGED File suffix added to OTU table file name once merged with metadata.

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
AddMetadataToTaxaTables()

Method Summary

Modifier and Type	Method and Description
protected void	addHitRatioToMetadata() Add Num_Hits/Num_Reads as Hit_Ratio column to the metadata file
void	cleanUp() For R to report taxa levels (not HumanN2 reports)
protected void	generateMergedTables() Create the merged metadata tables.
protected String	getMergedLine(String line) Return OTU table line with metadata row appended (both have PK = sample ID)
String	getSummary() Produce summary message with min, max, mean, and median hit ratios
void	runModule() This method matches records from the OTU table and the metadata file by matching the sample ID value in the very 1st column.

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

Methods inherited from class biolockj.module.BioModuleImpl

cacheInputFiles, 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

checkDependencies, getID, getModuleDir, getOutputDir, getPostRequisiteModules, getTempDir, init

Field Detail

HIT_RATIO

public static final String HIT_RATIO

Metadata column name for column that stores the calculation for: ParserModuleImpl.getOtuCountField()/ RegisterNumReads.getNumReadFieldName(): "Hit_Ratio".

See Also:

Constant Field Values

META_MERGED

public static final String META_MERGED

File suffix added to OTU table file name once merged with metadata.

See Also:

Constant Field Values

Constructor Detail

AddMetadataToTaxaTables

public AddMetadataToTaxaTables()

Method Detail

cleanUp

public void cleanUp()
             throws Exception

For R to report taxa levels (not HumanN2 reports)

Specified by:

cleanUp in interface BioModule

Overrides:

cleanUp in class BioModuleImpl

Throws:

Exception - thrown if any runtime error occurs

getSummary

public String getSummary()
                  throws Exception

Produce summary message with min, max, mean, and median hit ratios

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

This method matches records from the OTU table and the metadata file by matching the sample ID value in the very 1st column.

Specified by:

runModule in interface JavaModule

Specified by:

runModule in class JavaModuleImpl

Throws:

Exception - thrown if any runtime error occurs

addHitRatioToMetadata

protected void addHitRatioToMetadata()
                              throws Exception

Add Num_Hits/Num_Reads as Hit_Ratio column to the metadata file

Throws:

Exception - if unable to build the new metadata column

generateMergedTables

protected void generateMergedTables()
                             throws Exception

Create the merged metadata tables.

Throws:

Exception - if unable to build tables

getMergedLine

protected String getMergedLine(String line)
                        throws Exception

Return OTU table line with metadata row appended (both have PK = sample ID)

Parameters:

line - OTU table line

Returns:

OTU table line + metadata line

Throws:

Exception - if unable to create merged line