biolockj.module.report.otu

Class RemoveScarceOtuCounts

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.JavaModuleImpl

biolockj.module.report.otu.OtuCountModule

biolockj.module.report.otu.RemoveScarceOtuCounts

All Implemented Interfaces:

BioModule, JavaModule, ScriptModule, Comparable<BioModule>

public class RemoveScarceOtuCounts
extends OtuCountModule

This BioModule removes scarce OTUs not found in enough samples.
The OTU must be found in a configurable percentage of samples.

GUI Module Name

Remove Scarce 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
RemoveScarceOtuCounts()

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() Set the number of hits field.
protected static TreeMap<String,TreeSet<String>>	findScarceOtus(TreeMap<String,TreeMap<String,Long>> sampleOtuCounts, TreeSet<String> uniqueOtus, TreeMap<String,TreeSet<String>> scarceTaxa) Find the scarce OTUs that contain the key values in scarceTaxa.
protected TreeMap<String,TreeSet<String>>	findScarceTaxa(TreeMap<String,TreeMap<String,Long>> sampleOtuCounts, TreeSet<String> otus) Find scarce taxa found in less samples than the cutoff percentage: Config."report.scarceCountCutoff".
String	getSummary() Produce summary message with min, max, mean, and median number of reads.
protected TreeMap<String,TreeMap<String,Long>>	getUpdatedOtuCounts(TreeMap<String,TreeMap<String,Long>> sampleOtuCounts, TreeMap<String,TreeSet<String>> scarceOtus) Remove scarce OTUs from the sampleOtuCounts and return it.
protected void	logScarceOtus(Set<String> scarceOtus) Save a list of scarce OTUs to the module temp directory.
protected void	removeScarceOtuCounts(TreeMap<String,TreeMap<String,Long>> updatedOtuCounts) Output OTU count files with the updatedOtuCounts
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

RemoveScarceOtuCounts

public RemoveScarceOtuCounts()

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

Set the number of hits field.

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

findScarceTaxa

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

Find scarce taxa found in less samples than the cutoff percentage: Config."report.scarceCountCutoff". Return a map of these scare taxa and a set of samples that need to remove them.

Parameters:

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

otus - TreeSet of unique OTUs

Returns:

TreeMap(taxa, TreeSet(SampleIds))

Throws:

Exception - if errors occur

getUpdatedOtuCounts

protected TreeMap<String,TreeMap<String,Long>> getUpdatedOtuCounts(TreeMap<String,TreeMap<String,Long>> sampleOtuCounts,
                                                                   TreeMap<String,TreeSet<String>> scarceOtus)

Remove scarce OTUs from the sampleOtuCounts and return it.

Parameters:

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

scarceOtus - TreeMap(OTU, TreeSet(SampleId)) Scarce OTUs and the samples that list them

Returns:

TreeMap(SampleId, TreeMap(OTU, count)) sampleOtuCounts after scarce OTUs have been removed

logScarceOtus

protected void logScarceOtus(Set<String> scarceOtus)
                      throws Exception

Save a list of scarce OTUs to the module temp directory.

Parameters:

scarceOtus - OTUs found in too few samples

Throws:

Exception - if errors occur

removeScarceOtuCounts

protected void removeScarceOtuCounts(TreeMap<String,TreeMap<String,Long>> updatedOtuCounts)
                              throws Exception

Output OTU count files with the updatedOtuCounts

Parameters:

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

Throws:

Exception - if errors occur

findScarceOtus

protected static TreeMap<String,TreeSet<String>> findScarceOtus(TreeMap<String,TreeMap<String,Long>> sampleOtuCounts,
                                                                TreeSet<String> uniqueOtus,
                                                                TreeMap<String,TreeSet<String>> scarceTaxa)

Find the scarce OTUs that contain the key values in scarceTaxa.

Parameters:

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

uniqueOtus - TreeSet(OTU) contains all OTUs for all samples

scarceTaxa - TreeMap(taxa, TreeSet(SampleId)) contains scarce taxa and their associated samples

Returns:

TreeMap(OTU, TreeSet(SampleId)) contains scarce OTUs and their associated samples