biolockj.module.report.humann2

Class RemoveLowPathwayCounts

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.JavaModuleImpl

biolockj.module.report.humann2.Humann2CountModule

biolockj.module.report.humann2.RemoveLowPathwayCounts

All Implemented Interfaces:

BioModule, JavaModule, ScriptModule, Comparable<BioModule>

public class RemoveLowPathwayCounts
extends Humann2CountModule

This BioModule set low Pathway counts below a configured threshold to zero.
These low sample counts are assumed to be miscategorized or genomic contamination.

GUI Module Name

Remove Low Pathway Counts

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
RemoveLowPathwayCounts()

Method Summary

Modifier and Type	Method and Description
void	checkDependencies() Validate module dependencies: Require Config. exists Require Config. is positive integer Require Config. is positive integer Verify Config. is positive integer if set
String	getSummary() Produce summary message with min, max, mean, and median number of pathways.
protected void	logLowCountPathways(TreeMap<String,TreeSet<String>> map) Save a list of low count pathways to the module temp directory.
protected TreeMap<String,TreeSet<String>>	removeLowPathwayCounts(File file) Remove Pathway Counts below the Config."report.minCount"
void	runModule() This method executes the modules primary Java routine.

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

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, 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

Constructor Detail

RemoveLowPathwayCounts

public RemoveLowPathwayCounts()

Method Detail

checkDependencies

public void checkDependencies()
                       throws Exception

Description copied from class: ScriptModuleImpl

Validate module dependencies:

• Require Config. exists
• Require Config. is positive integer
• Require Config. is positive integer
• Verify Config. is positive integer if set

Specified by:

checkDependencies in interface BioModule

Overrides:

checkDependencies in class Humann2CountModule

Throws:

Exception - thrown if missing or invalid dependencies are found

getSummary

public String getSummary()
                  throws Exception

Produce summary message with min, max, mean, and median number of pathways.

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

logLowCountPathways

protected void logLowCountPathways(TreeMap<String,TreeSet<String>> map)
                            throws Exception

Save a list of low count pathways to the module temp directory.

Parameters:

map - TreeMap(sampleId, TreeSet(Pathway)) of Pathways found in too few samples

Throws:

Exception - if errors occur

removeLowPathwayCounts

protected TreeMap<String,TreeSet<String>> removeLowPathwayCounts(File file)
                                                          throws Exception

Remove Pathway Counts below the Config."report.minCount"

Parameters:

file - Input file

Returns:

TreeMap(SampleId, TreeMap(Pathway)) Map removed pathways to sample ID

Throws:

Exception - if errors occur