biolockj.module.report.humann2

Class AddMetadataToPathwayTables

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.JavaModuleImpl

biolockj.module.report.humann2.Humann2CountModule

biolockj.module.report.humann2.AddMetadataToPathwayTables

All Implemented Interfaces:

BioModule, JavaModule, ScriptModule, Comparable<BioModule>

public class AddMetadataToPathwayTables
extends Humann2CountModule

This BioModule is used to add metadata columns to the HumanN2 pathway abundance, pathway coverage, and gene family tables.

GUI Module Name

Add Metadata to Pathway 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.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
AddMetadataToPathwayTables()

Method Summary

Modifier and Type	Method and Description
void	cleanUp() For R to report HumanN2 reports instead of taxa levels
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 Pathway Abundance table and the metadata file by matching the sample ID value in the very 1st column (regardless of column title). Set

Methods inherited from class biolockj.module.report.humann2.Humann2CountModule

checkDependencies, getInputFiles, getPreRequisiteModules, isHumann2CountModule, 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, 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

getID, getModuleDir, getOutputDir, getPostRequisiteModules, getTempDir, init

Constructor Detail

AddMetadataToPathwayTables

public AddMetadataToPathwayTables()

Method Detail

cleanUp

public void cleanUp()
             throws Exception

For R to report HumanN2 reports instead of taxa levels

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 Pathway Abundance table and the metadata file by matching the sample ID value in the very 1st column (regardless of column title).

Set

Specified by:

runModule in interface JavaModule

Specified by:

runModule in class JavaModuleImpl

Throws:

Exception - thrown if any runtime error occurs

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