biolockj.module.classifier.r16s

Class RdpClassifier

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.SeqModuleImpl

biolockj.module.classifier.ClassifierModuleImpl

biolockj.module.classifier.r16s.RdpClassifier

All Implemented Interfaces:

BioModule, ClassifierModule, DatabaseModule, ScriptModule, SeqModule, Comparable<BioModule>

public class RdpClassifier
extends ClassifierModuleImpl

This BioModule uses RDP to assign taxonomy to 16s sequences.

GUI Module Name

RDP Classifier

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	FUNCTION_RDP Name of the RdpClassifier bash script function used to assign taxonomy: "runRdp"
protected static String	RDP_DB Config File property used to define an alternate RDP database file: "rdp.db"
protected static String	RDP_JAR Config File property for RDP java executable JAR: "rdp.jar"
protected static String	RDP_PARAMS Config List property for RDP java executable JAR runtime params: "exe.rdpParams"

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
RdpClassifier()

Method Summary

Modifier and Type	Method and Description
List<List<String>>	buildScript(List<File> files) Build bash script lines to classify unpaired reads with RDP.
void	checkDependencies() Validate module dependencies: Call ClassifierModuleImpl.getClassifierExe() to verify the executable Call ClassifierModuleImpl.getClassifierParams() to verify the runtime parameters are valid Call ClassifierModuleImpl.validateModuleOrder() to validate module configuration order.
String	getClassifierExe() RDP uses java to run a JAR file, so no special command is required
List<String>	getClassifierParams() Do not accept -t to define a database, since that instead requires the specific property: "rdp.db"
File	getDB() Return database directory, if multiple databases are configured, they must share a common parent directory and the common parent directory is returned by this method.
List<String>	getPreRequisiteModules() If paired reads found, add prerequisite: PearMergeReads.
List<String>	getWorkerScriptFunctions() This method generates the required bash functions: "runRdp"

Methods inherited from class biolockj.module.classifier.ClassifierModuleImpl

getClassifierType, getPostRequisiteModules, getSummary, validateModuleOrder

Methods inherited from class biolockj.module.SeqModuleImpl

getInputFiles, getSeqFiles, isValidInputModule

Methods inherited from class biolockj.module.ScriptModuleImpl

buildScriptForPairedReads, executeTask, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getTimeout, hasScripts

Methods inherited from class biolockj.module.BioModuleImpl

cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getFileCache, getID, getModuleDir, getOutputDir, 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.SeqModule

getSeqFiles

Methods inherited from interface biolockj.module.ScriptModule

buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout

Methods inherited from interface biolockj.module.BioModule

cleanUp, executeTask, getID, getInputFiles, getModuleDir, getOutputDir, getTempDir, init, isValidInputModule

Field Detail

FUNCTION_RDP

protected static final String FUNCTION_RDP

Name of the RdpClassifier bash script function used to assign taxonomy: "runRdp"

See Also:

Constant Field Values

RDP_DB

protected static final String RDP_DB

Config File property used to define an alternate RDP database file: "rdp.db"

See Also:

Constant Field Values

RDP_JAR

protected static final String RDP_JAR

Config File property for RDP java executable JAR: "rdp.jar"

See Also:

Constant Field Values

RDP_PARAMS

protected static final String RDP_PARAMS

Config List property for RDP java executable JAR runtime params: "exe.rdpParams"

See Also:

Constant Field Values

Constructor Detail

RdpClassifier

public RdpClassifier()

Method Detail

buildScript

public List<List<String>> buildScript(List<File> files)
                               throws Exception

Build bash script lines to classify unpaired reads with RDP. The inner list contains the bash script lines required to classify 1 sample (call java to run RDP jar on sample).

Example line: "java -jar $RDP_PATH t /database/silva128/rRNAClassifier.properties -o ./output/sample42.fasta_reported.tsv ./input/sample42.fasta"

Specified by:

buildScript in interface ScriptModule

Specified by:

buildScript in class ScriptModuleImpl

Parameters:

files - Files in the input directory that contain only forward reads

Returns:

Nested list of bash scripts lines

Throws:

Exception - if unable to generate script lines

checkDependencies

public void checkDependencies()
                       throws Exception

Description copied from class: ClassifierModuleImpl

Validate module dependencies:

• Call ClassifierModuleImpl.getClassifierExe() to verify the executable
• Call ClassifierModuleImpl.getClassifierParams() to verify the runtime parameters are valid
• Call ClassifierModuleImpl.validateModuleOrder() to validate module configuration order.
• Call BioModule.checkDependencies() to validate script dependencies.

Specified by:

checkDependencies in interface BioModule

Overrides:

checkDependencies in class ClassifierModuleImpl

Throws:

Exception - thrown if missing or invalid dependencies are found

getClassifierExe

public String getClassifierExe()
                        throws Exception

RDP uses java to run a JAR file, so no special command is required

Specified by:

getClassifierExe in interface ClassifierModule

Specified by:

getClassifierExe in class ClassifierModuleImpl

Returns:

Command to execute classifier program

Throws:

Exception - if the classifier program undefined or invalid

getClassifierParams

public List<String> getClassifierParams()
                                 throws Exception

Do not accept -t to define a database, since that instead requires the specific property: "rdp.db"

Specified by:

getClassifierParams in interface ClassifierModule

Specified by:

getClassifierParams in class ClassifierModuleImpl

Returns:

Runtime parameters

Throws:

Exception - thrown if parameters defined are invalid

getDB

public File getDB()
           throws Exception

Description copied from interface: DatabaseModule

Return database directory, if multiple databases are configured, they must share a common parent directory and the common parent directory is returned by this method.

Specified by:

getDB in interface DatabaseModule

Specified by:

getDB in class ClassifierModuleImpl

Returns:

Database directory

Throws:

Exception - thrown if any runtime error occurs

getPreRequisiteModules

public List<String> getPreRequisiteModules()
                                    throws Exception

If paired reads found, add prerequisite: PearMergeReads.

Specified by:

getPreRequisiteModules in interface BioModule

Overrides:

getPreRequisiteModules in class BioModuleImpl

Returns:

List of BioModule Class Names

Throws:

Exception - if invalid Class names are returned as prerequisites

getWorkerScriptFunctions

public List<String> getWorkerScriptFunctions()
                                      throws Exception

This method generates the required bash functions: "runRdp"

Specified by:

getWorkerScriptFunctions in interface ScriptModule

Overrides:

getWorkerScriptFunctions in class ScriptModuleImpl

Returns:

Bash script lines for the functions

Throws:

Exception - if errors occur