biolockj.module.report.otu

Class RemoveLowOtuCounts

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.JavaModuleImpl

biolockj.module.report.otu.OtuCountModule

biolockj.module.report.otu.RemoveLowOtuCounts

All Implemented Interfaces:

BioModule, JavaModule, ScriptModule, Comparable<BioModule>

public class RemoveLowOtuCounts
extends OtuCountModule

This BioModule set low OTU counts below a configured threshold to zero.
These low sample counts are assumed to be miscategorized or contaminents.

GUI Module Name

Remove Low OTU 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
RemoveLowOtuCounts()

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
void	cleanUp() Update ParserModuleImpl OTU_COUNT field name.
String	getSummary() Produce summary message with min, max, mean, and median number of reads.
protected void	logLowCountOtus(TreeMap<String,TreeSet<String>> lowCountOtus) Save a list of low count OTUs to the module temp directory.
protected TreeMap<String,TreeSet<String>>	removeLowOtuCounts(TreeMap<String,TreeMap<String,Long>> sampleOtuCounts) Remove OTUs below the Config.
void	runModule() This method executes the modules primary Java routine.

Methods inherited from class biolockj.module.report.otu.OtuCountModule

getInputFiles, isOtuModule, 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, getPreRequisiteModules, 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, getPreRequisiteModules, getTempDir, init

Constructor Detail

RemoveLowOtuCounts

public RemoveLowOtuCounts()

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 ScriptModuleImpl

Throws:

Exception - thrown if missing or invalid dependencies are found

cleanUp

public void cleanUp()
             throws Exception

Update ParserModuleImpl OTU_COUNT field name.

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 number of reads.

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

logLowCountOtus

protected void logLowCountOtus(TreeMap<String,TreeSet<String>> lowCountOtus)
                        throws Exception

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

Parameters:

lowCountOtus - TreeMap(sampleId, TreeSet(OTU)) of OTUs found in too few samples

Throws:

Exception - if errors occur

removeLowOtuCounts

protected TreeMap<String,TreeSet<String>> removeLowOtuCounts(TreeMap<String,TreeMap<String,Long>> sampleOtuCounts)
                                                      throws Exception

Remove OTUs below the Config.

Parameters:

sampleOtuCounts - TreeMap(SampleId, TreeMap(OTU, count)) OTU counts for every sample

Returns:

TreeMap(SampleId, TreeMap(OTU, count)) Updated sampleOtuCounts after removal of low counts.

Throws:

Exception - if errors occur