biolockj.module.implicit.parser.wgs

Class Kraken2Parser

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.JavaModuleImpl

biolockj.module.implicit.parser.ParserModuleImpl

biolockj.module.implicit.parser.wgs.KrakenParser

biolockj.module.implicit.parser.wgs.Kraken2Parser

All Implemented Interfaces:

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

public class Kraken2Parser
extends KrakenParser

This BioModules parses KrakenClassifier output reports to build standard OTU abundance tables.

GUI Module Name

Kraken2 Parser

Field Summary

Fields inherited from class biolockj.module.implicit.parser.ParserModuleImpl

NUM_OTUS

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
Kraken2Parser()

Method Summary

Modifier and Type	Method and Description
protected void	parseSample(File file) Construct a new KrakenNode
void	parseSamples() Parse all Kraken2Classifier reports in the input directory. Cache the leaf counts Build an Kraken2Node for each line. If ParserModuleImpl.isValid(OtuNode), Create ParsedSample for the OtuNodeImpl.getSampleId() if not yet created.

Methods inherited from class biolockj.module.implicit.parser.wgs.KrakenParser

addOtuNode, getCitationString, getDescription

Methods inherited from class biolockj.module.implicit.parser.ParserModuleImpl

addParsedSample, buildOtuCountFiles, checkDependencies, getDepricatedOtuCountFields, getHitsPerSample, getOtuCountField, getParsedSample, getParsedSamples, getSampleIds, getSummary, getUniqueOtus, isValid, runModule, setNumHitsFieldName, validateModuleOrder

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.api.ApiModule

getDescription, getDetails, getMenuPlacement, getPropType, getTitle, isValidProp, listProps

Methods inherited from interface biolockj.module.BioModule

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

Methods inherited from interface biolockj.module.JavaModule

moduleComplete, moduleFailed

Methods inherited from interface biolockj.module.ScriptModule

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

Constructor Detail

Kraken2Parser

public Kraken2Parser()

Method Detail

parseSample

protected void parseSample(File file)
                    throws Exception

Description copied from class: KrakenParser

Construct a new KrakenNode

Overrides:

parseSample in class KrakenParser

Parameters:

file - KrakenClassifier output file

Throws:

Exception - if any errors occur

parseSamples

public void parseSamples()
                  throws Exception

Parse all Kraken2Classifier reports in the input directory.
Cache the leaf counts Build an Kraken2Node for each line.
If ParserModuleImpl.isValid(OtuNode),

1. Create ParsedSample for the OtuNodeImpl.getSampleId() if not yet created.
2. Add the OtuNodeImpl.getCount() (1) to ParsedSample OTU count.

Sample Kraken report line (head 7A_reported.tsv) :
FCC6MMAACXX:8:1101:1968:2100#GTATTCTC/1 d__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_vulgatus

Specified by:

parseSamples in interface ParserModule

Overrides:

parseSamples in class KrakenParser

Throws:

Exception - if error occurs while parsing classifier reports