biolockj.module.implicit.parser.r16s

Class RdpParser

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.JavaModuleImpl

biolockj.module.implicit.parser.ParserModuleImpl

biolockj.module.implicit.parser.r16s.RdpParser

All Implemented Interfaces:

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

public class RdpParser
extends ParserModuleImpl
implements ApiModule

This BioModule parses RDP output files to build standard OTU abundance tables.

GUI Module Name

RDP 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
RdpParser()

Method Summary

Modifier and Type	Method and Description
String	getCitationString() At a minimum, this should return the name and/or url for the wrapped tool.
String	getDescription() Briefly describe what this module does.
protected boolean	isValid(OtuNode node) If RdpNode.getScore() is above the Config., continue with the standard OtuNode validation.
void	parseSamples() Parse all RdpClassifier reports in the input directory. Build an RdpNode for each line. If isValid(OtuNode), Create ParsedSample for the OtuNodeImpl.getSampleId() if not yet created.
String	version() Changes to a module class should be accompanied by a increment in version.

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

addOtuNode, addParsedSample, buildOtuCountFiles, checkDependencies, getDepricatedOtuCountFields, getHitsPerSample, getOtuCountField, getParsedSample, getParsedSamples, getSampleIds, getSummary, getUniqueOtus, 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

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

RdpParser

public RdpParser()

Method Detail

parseSamples

public void parseSamples()
                  throws Exception

Parse all RdpClassifier reports in the input directory.
Build an RdpNode for each line.
If isValid(OtuNode),

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

Sample QIIME report line (head 7A_reported.tsv):
FCABK7W:1:2105:21787:12788#/1 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Clostridia class 1.0 Clostridiales order 1.0 Ruminococcaceae family 1.0 Faecalibacterium genus 1.0

Specified by:

parseSamples in interface ParserModule

Specified by:

parseSamples in class ParserModuleImpl

Throws:

Exception - if error occurs while parsing classifier reports

isValid

protected boolean isValid(OtuNode node)

If RdpNode.getScore() is above the Config., continue with the standard OtuNode validation.

Overrides:

isValid in class ParserModuleImpl

Parameters:

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

Returns:

boolean if OtuNode is valid

getDescription

public String getDescription()

Description copied from interface: ApiModule

Briefly describe what this module does. A more detailed description may be returned by getDetails.

Specified by:

getDescription in interface ApiModule

Returns:

getCitationString

public String getCitationString()

Description copied from interface: ApiModule

At a minimum, this should return the name and/or url for the wrapped tool. For BioLockJ home-grown modules, it can cite BioLockJ and give the current version. Ideally this will include the version for the wrapped tool. Tool version may require using a stored variable that can be filled in during execution; and the string that is returned pre-execution may not have the version.

Specified by:

getCitationString in interface ApiModule

Returns:

version

public String version()

Description copied from interface: BioModule

Changes to a module class should be accompanied by a increment in version. The is a string and open form, but using the major.minor.patch semantic versioning is recommended.

Specified by:

version in interface BioModule

Returns: