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.Kraken2Parser

All Implemented Interfaces:

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

public class Kraken2Parser
extends ParserModuleImpl

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.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
Kraken2Parser()

Method Summary

Modifier and Type	Method and Description
void	parseSamples() Parse all Kraken2Classifier reports in the input directory. 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.ParserModuleImpl

addOtuNode, buildOtuCountFiles, checkDependencies, getDepricatedOtuCountFields, getOtuCountField, getParsedSample, getSummary, isValid, runModule, setNumHitsFieldName, validateModuleOrder

Methods inherited from class biolockj.module.JavaModuleImpl

buildScript, executeTask, getSource, getWorkerScriptFunctions, isValidInputModule, 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, cleanUp, compareTo, equals, findModuleInputFiles, getFileCache, getID, getInputFiles, 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.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, getID, getInputFiles, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getTempDir, init, isValidInputModule

Constructor Detail

Kraken2Parser

public Kraken2Parser()

Method Detail

parseSamples

public void parseSamples()
                  throws Exception

Parse all Kraken2Classifier reports in the input directory.
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_1_reported.tsv) :
d__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales 20094

Specified by:

parseSamples in interface ParserModule

Specified by:

parseSamples in class ParserModuleImpl

Throws:

Exception - if error occurs while parsing classifier reports