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:

ApiModule, BioModule, JavaModule, ScriptModule, Comparable<BioModule>

public class AddMetadataToTaxaTables
extends TaxaCountModule
implements ApiModule

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.BioModule

LOG_DIR, MAIN_SCRIPT_PREFIX, NO_VERSION, OUTPUT_DIR, RES_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.
String	getCitationString() At a minimum, this should return the name and/or url for the wrapped tool.
String	getDescription() Briefly describe what this module does.
String	getDetails() All child classes from this class have this pre-req.
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, getDockerImageName, getDockerImageOwner, getDockerImageTag, getWorkerScriptFunctions, markStatus, moduleComplete, moduleFailed, runBioLockJ_CMD

Methods inherited from class biolockj.module.ScriptModuleImpl

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

Methods inherited from class biolockj.module.BioModuleImpl

addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getFileCache, getID, getLogDir, getMenuPlacement, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPropDefault, getPropDescMap, getPropType, getPropTypeMap, getResourceDir, getTempDir, getTitle, hashCode, init, listProps, setAlias, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface biolockj.api.ApiModule

getDescription, getMenuPlacement, getPropType, getTitle, isValidProp, listProps

Methods inherited from interface biolockj.module.BioModule

checkDependencies, executeTask, getAlias, getDockerImageName, getDockerImageOwner, getDockerImageTag, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getResourceDir, getTempDir, init, isValidInputModule, setAlias, version

Methods inherited from interface biolockj.module.ScriptModule

buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout

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

getDescription

public String getDescription()

Description copied from interface: ApiModule

Briefly describe what this module does. A more detailed description may be returned by getDetails.

Specified by:

getDescription in interface ApiModule

Returns:

getDetails

public String getDetails()
                  throws API_Exception

Description copied from class: TaxaCountModule

All child classes from this class have this pre-req.

Specified by:

getDetails in interface ApiModule

Overrides:

getDetails in class TaxaCountModule

Returns:

Throws:

API_Exception

getCitationString

public String getCitationString()

Description copied from interface: ApiModule

At a minimum, this should return the name and/or url for the wrapped tool. For BioLockJ home-grown modules, it can cite BioLockJ and give the current version. Ideally this will include the version for the wrapped tool. Tool version may require using a stored variable that can be filled in during execution; and the string that is returned pre-execution may not have the version.

Specified by:

getCitationString in interface ApiModule

Returns: