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:

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

public class RdpClassifier
extends ClassifierModuleImpl
implements ApiModule

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"
static String	HIER_COUNTS
static String	HIER_SUFFIX
protected static String	JAVA_PARAMS Config List property: "rdp.javaParams" The parameters for the call to java when running rdp.
protected static String	RDP_DB Config File property used to define an alternate RDP database file: "rdp.db"
protected static String	RDP_DOCKER_JAR Config File property for RDP java executable jar WHEN RUNNING IN DOCKER: "rdp.containerJar" This is the path in the default docker container.
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: "rdp.params"

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
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	getCitationString() At a minimum, this should return the name and/or url for the wrapped tool.
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" If "rdp.hierCounts" is true, then skip any parameter for it here, it will added per file.
(package private) String	getConfThreshold()
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.
String	getDescription() Briefly describe what this module does.
String	getDockerImageName() Get the docker image to use for this module.
String	getDockerImageOwner() Get the name of the docker hub user that owns the image to use for this module.
String	getDockerImageTag() Get the version / tag to use for the docker image.
List<String>	getPostRequisiteModules() This method returns the corresponding Parser module associated with the classifier.
List<String>	getPreRequisiteModules() If paired reads found, add prerequisite: PearMergeReads.
List<String>	getWorkerScriptFunctions() This method generates the required bash functions: "runRdp"
String	version() Changes to a module class should be accompanied by a increment in version.

Methods inherited from class biolockj.module.classifier.ClassifierModuleImpl

getClassifierType, getDbCache, getSummary, setDbCache, 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, isValidProp

Methods inherited from class biolockj.module.BioModuleImpl

addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getDetails, getFileCache, getID, getLogDir, getMenuPlacement, getMetadata, getModuleDir, getOutputDir, 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

cleanUp, executeTask, getAlias, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, getPropDefault, getResourceDir, getSummary, getTempDir, init, isValidInputModule, setAlias

Methods inherited from interface biolockj.module.SeqModule

getSeqFiles

Methods inherited from interface biolockj.module.ScriptModule

buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout

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_DOCKER_JAR

protected static final String RDP_DOCKER_JAR

Config File property for RDP java executable jar WHEN RUNNING IN DOCKER: "rdp.containerJar" This is the path in the default docker container.

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: "rdp.params"

See Also:

Constant Field Values

HIER_COUNTS

public static final String HIER_COUNTS

See Also:

Constant Field Values

HIER_SUFFIX

public static final String HIER_SUFFIX

See Also:

Constant Field Values

JAVA_PARAMS

protected static final String JAVA_PARAMS

Config List property: "rdp.javaParams" The parameters for the call to java when running rdp.

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 ConfigException

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:

ConfigException - if Configuration errors are thrown

getClassifierParams

public List<String> getClassifierParams()
                                 throws ConfigException

Do not accept -t to define a database, since that instead requires the specific property: "rdp.db"
If "rdp.hierCounts" is true, then skip any parameter for it here, it will added per file.

Specified by:

getClassifierParams in interface ClassifierModule

Specified by:

getClassifierParams in class ClassifierModuleImpl

Returns:

Runtime parameters

Throws:

ConfigException - if Configuration errors are thrown

getDB

public File getDB()
           throws ConfigPathException,
                  ConfigNotFoundException,
                  DockerVolCreationException

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:

ConfigPathException - if path is defined but does not exists

ConfigNotFoundException - if DB property is undefined and the default DB is not included in the module runtime env

DockerVolCreationException

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

getDockerImageOwner

public String getDockerImageOwner()

Description copied from interface: BioModule

Get the name of the docker hub user that owns the image to use for this module. Docker images from docker hub are specified using this syntax: /:

Specified by:

getDockerImageOwner in interface BioModule

Overrides:

getDockerImageOwner in class BioModuleImpl

Returns:

getDockerImageName

public String getDockerImageName()

Description copied from interface: BioModule

Get the docker image to use for this module. The owner and version/tag are specificed separately; this is just the image name. Docker images from docker hub are specified using this syntax: /:

Specified by:

getDockerImageName in interface BioModule

Returns:

getDockerImageTag

public String getDockerImageTag()

Description copied from interface: BioModule

Get the version / tag to use for the docker image. Docker images from docker hub are specified using this syntax: /:

Specified by:

getDockerImageTag in interface BioModule

Overrides:

getDockerImageTag in class BioModuleImpl

Returns:

getConfThreshold

String getConfThreshold()
                 throws ConfigNotFoundException,
                        ConfigFormatException

Throws:

ConfigNotFoundException

ConfigFormatException

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:

getPostRequisiteModules

public List<String> getPostRequisiteModules()
                                     throws Exception

Description copied from class: ClassifierModuleImpl

This method returns the corresponding Parser module associated with the classifier. The Parser module name is built using the same prefix used in the Classifier module

For example RdpClassifier, will return the RdpParser.

Specified by:

getPostRequisiteModules in interface BioModule

Overrides:

getPostRequisiteModules in class ClassifierModuleImpl

Returns:

List of BioModules

Throws:

Exception - if invalid Class names are returned as post-requisites