biolockj.module.implicit.parser

Class ParserModuleImpl

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.JavaModuleImpl

biolockj.module.implicit.parser.ParserModuleImpl

All Implemented Interfaces:

BioModule, ParserModule, JavaModule, ScriptModule, Comparable<BioModule>

Direct Known Subclasses:

Humann2Parser, KrakenParser, Metaphlan2Parser, QiimeParser, RdpParser

public abstract class ParserModuleImpl
extends JavaModuleImpl
implements ParserModule

Parser BioModules read ClassifierModule output to build standardized OTU count tables. This class provides the default abstract implementation.

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	NUM_OTUS Metadata column name for column that holds number of OTU hits after any biolockj.module.implicit.parser module executes: "OTU_COUNT"

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
ParserModuleImpl()

Method Summary

Modifier and Type	Method and Description
void	addOtuNode(OtuNode node) Each sample with taxonomic assignments from a ClassifierModule is parsed by ParserModule.parseSamples() to produce a ParsedSample.
protected void	addParsedSample(ParsedSample parsedSample) Add ParsedSample to parser cache
void	buildOtuCountFiles() After ParserModule.parseSamples() completes, this method builds the OTU count files.
void	checkDependencies() Execute validateModuleOrder() to validate module configuration order.
static Set<String>	getDepricatedOtuCountFields() Getter for depricatedOtuCountFields
protected Map<String,String>	getHitsPerSample() Simple getter for hitsPerSample map
static String	getOtuCountField() Getter for otuCountField
ParsedSample	getParsedSample(String sampleId) After ParserModule.parseSamples() completes, this method can be called to get a ParsedSample by its sample ID.
protected TreeSet<ParsedSample>	getParsedSamples() Simple getter for TreeSet of ParsedSamples
protected Set<String>	getSampleIds() Simple getter for Set of Sample IDs output by the module
String	getSummary() Produce summary message with min, max, mean, and median number of reads.
protected Set<String>	getUniqueOtus() Simple getter for Set of unique OTU names output by the module
protected boolean	isValid(OtuNode node) Some ClassifierModules can include taxonomy level identifiers without an OTU name in the sample report files.
abstract void	parseSamples() Parse ClassifierModule output to build ParsedSamples.
void	runModule() Parsers execute a task with 3 core functions: parseSamples() - generates ParsedSamples buildOtuCountFiles() - builds OTU tree tables from ParsedSamples
static void	setNumHitsFieldName(String name) When a module modifies the number of hits, the new counts must replace the old count fields.
protected void	validateModuleOrder() Validate that no biolockj.module.seq modules run after this parser unless a new classifier branch is started.

Methods inherited from class biolockj.module.JavaModuleImpl

buildScript, executeTask, getDockerImageName, getDockerImageOwner, getDockerImageTag, getWorkerScriptFunctions, isValidInputModule, markStatus, moduleComplete, moduleFailed, runBioLockJ_CMD

Methods inherited from class biolockj.module.ScriptModuleImpl

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

Methods inherited from class biolockj.module.BioModuleImpl

addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getDetails, getFileCache, getID, getInputFiles, getLogDir, getMenuPlacement, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, 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.module.JavaModule

moduleComplete, moduleFailed

Methods inherited from interface biolockj.module.ScriptModule

buildScript, buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout, getWorkerScriptFunctions

Methods inherited from interface biolockj.module.BioModule

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

Field Detail

NUM_OTUS

protected static final String NUM_OTUS

Metadata column name for column that holds number of OTU hits after any biolockj.module.implicit.parser module executes: "OTU_COUNT"

See Also:

Constant Field Values

Constructor Detail

ParserModuleImpl

public ParserModuleImpl()

Method Detail

addOtuNode

public void addOtuNode(OtuNode node)
                throws Exception

Description copied from interface: ParserModule

Each sample with taxonomic assignments from a ClassifierModule is parsed by ParserModule.parseSamples() to produce a ParsedSample. As each file is processed, this method is called to add the OtuNode to the ParsedSample with the same sample ID (if valid).

Specified by:

addOtuNode in interface ParserModule

Parameters:

node - OtuNode

Throws:

Exception - if unable to add the OTU node

buildOtuCountFiles

public void buildOtuCountFiles()
                        throws Exception

Description copied from interface: ParserModule

After ParserModule.parseSamples() completes, this method builds the OTU count files.

Specified by:

buildOtuCountFiles in interface ParserModule

Throws:

Exception - if error occurs while building OTU tables

checkDependencies

public void checkDependencies()
                       throws Exception

Execute validateModuleOrder() to validate module configuration order.

Specified by:

checkDependencies in interface BioModule

Overrides:

checkDependencies in class ScriptModuleImpl

Throws:

Exception - thrown if missing or invalid dependencies are found

getParsedSample

public ParsedSample getParsedSample(String sampleId)

Description copied from interface: ParserModule

After ParserModule.parseSamples() completes, this method can be called to get a ParsedSample by its sample ID.

Specified by:

getParsedSample in interface ParserModule

Parameters:

sampleId - Sample ID

Returns:

ParsedSample with the given sampleId

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

parseSamples

public abstract void parseSamples()
                           throws Exception

Description copied from interface: ParserModule

Parse ClassifierModule output to build ParsedSamples.

Specified by:

parseSamples in interface ParserModule

Throws:

Exception - if error occurs while parsing classifier reports

runModule

public void runModule()
               throws Exception

Parsers execute a task with 3 core functions:

1. parseSamples() - generates ParsedSamples
2. buildOtuCountFiles() - builds OTU tree tables from ParsedSamples

Specified by:

runModule in interface JavaModule

Specified by:

runModule in class JavaModuleImpl

Throws:

Exception - thrown if any runtime error occurs

addParsedSample

protected void addParsedSample(ParsedSample parsedSample)
                        throws Exception

Add ParsedSample to parser cache

Parameters:

parsedSample - ParsedSample

Throws:

Exception - if method is used to add a duplicate sample

getHitsPerSample

protected Map<String,String> getHitsPerSample()

Simple getter for hitsPerSample map

Returns:

Map {key=SampleId, val=#hits}

getParsedSamples

protected TreeSet<ParsedSample> getParsedSamples()

Simple getter for TreeSet of ParsedSamples

Returns:

TreeSet of ParsedSamples

getSampleIds

protected Set<String> getSampleIds()

Simple getter for Set of Sample IDs output by the module

Returns:

Set of Sample IDs

getUniqueOtus

protected Set<String> getUniqueOtus()

Simple getter for Set of unique OTU names output by the module

Returns:

Set of unique OTU names

isValid

protected boolean isValid(OtuNode node)
                   throws Exception

Some ClassifierModules can include taxonomy level identifiers without an OTU name in the sample report files. This method verifies the node exists, has a valid sample ID, and that no empty String OTU names are reported.

Parameters:

node - OtuNode build from 1 line of a ClassifierModule output file

Returns:

boolean if OtuNode is valid

Throws:

Exception - if errors occur checking if node is valid

validateModuleOrder

protected void validateModuleOrder()
                            throws Exception

Validate that no biolockj.module.seq modules run after this parser unless a new classifier branch is started.

Throws:

Exception - if modules are out of order

getDepricatedOtuCountFields

public static Set<String> getDepricatedOtuCountFields()

Getter for depricatedOtuCountFields

Returns:

depricatedOtuCountFields

getOtuCountField

public static String getOtuCountField()

Getter for otuCountField

Returns:

otuCountField

setNumHitsFieldName

public static void setNumHitsFieldName(String name)
                                throws Exception

When a module modifies the number of hits, the new counts must replace the old count fields.

Parameters:

name - Name of new number of hits metadata field

Throws:

Exception - if null value passed