biolockj.module.implicit.parser

Interface ParserModule

All Superinterfaces:

BioModule, JavaModule, ScriptModule

All Known Implementing Classes:

Humann2Parser, Kraken2Parser, KrakenParser, Metaphlan2Parser, ParserModuleImpl, QiimeParser, RdpParser

public interface ParserModule
extends JavaModule

This interface defines the required methods to parse ClassifierModule output. Each BioLockJ ClassifierModule implementation must have a corresponding ParserModule that understands the classifier output file format to extract the OTUs assigned to each sample. Parser BioModules read ClassifierModule output to build a single OTU count files for each sample using a standard format.

Field Summary

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

Method Summary

Modifier and Type	Method and Description
void	addOtuNode(OtuNode node) Each sample with taxonomic assignments from a ClassifierModule is parsed by parseSamples() to produce a ParsedSample.
void	buildOtuCountFiles() After parseSamples() completes, this method builds the OTU count files.
ParsedSample	getParsedSample(String sampleId) After parseSamples() completes, this method can be called to get a ParsedSample by its sample ID.
void	parseSamples() Parse ClassifierModule output to build ParsedSamples.

Methods inherited from interface biolockj.module.JavaModule

moduleComplete, moduleFailed, runModule

Methods inherited from interface biolockj.module.ScriptModule

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

Methods inherited from interface biolockj.module.BioModule

checkDependencies, cleanUp, executeTask, getID, getInputFiles, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getSummary, getTempDir, init, isValidInputModule

Method Detail

addOtuNode

void addOtuNode(OtuNode node)
         throws Exception

Each sample with taxonomic assignments from a ClassifierModule is parsed by 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).

Parameters:

node - OtuNode

Throws:

Exception - if unable to add the OTU node

buildOtuCountFiles

void buildOtuCountFiles()
                 throws Exception

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

Throws:

Exception - if error occurs while building OTU tables

getParsedSample

ParsedSample getParsedSample(String sampleId)

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

Parameters:

sampleId - Sample ID

Returns:

ParsedSample with the given sampleId

parseSamples

void parseSamples()
           throws Exception

Parse ClassifierModule output to build ParsedSamples.

Throws:

Exception - if error occurs while parsing classifier reports