biolockj.module.implicit.parser.wgs

Class Metaphlan2Parser

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.JavaModuleImpl

biolockj.module.implicit.parser.ParserModuleImpl

biolockj.module.implicit.parser.wgs.Metaphlan2Parser

All Implemented Interfaces:

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

public class Metaphlan2Parser
extends ParserModuleImpl

This BioModules parses Metaphlan2Classifier output reports to build standard OTU abundance tables.

GUI Module Name

MetaPhlAn2 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
Metaphlan2Parser()

Method Summary

Modifier and Type	Method and Description
void	parseSamples() To parse the taxonomy level reports output by Metaphlan2Classifier: 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

Metaphlan2Parser

public Metaphlan2Parser()

Method Detail

parseSamples

public void parseSamples()
                  throws Exception

To parse the taxonomy level reports output by Metaphlan2Classifier:

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

Sample Metaphlan2 report line (head 7A_1_reported.tsv) :
#SampleID Metaphlan22_Analysis #clade_name relative_abundance coverage average_genome_length_in_the_clade estimated_number_of_reads_from_the_clade k__Bacteria|p__Bacteroidetes 14.68863 0.137144143537 4234739 580770

Specified by:

parseSamples in interface ParserModule

Specified by:

parseSamples in class ParserModuleImpl

Throws:

Exception - if error occurs while parsing classifier reports