biolockj.module.classifier.wgs

Class KrakenClassifier

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.SeqModuleImpl

biolockj.module.classifier.ClassifierModuleImpl

biolockj.module.classifier.wgs.KrakenClassifier

All Implemented Interfaces:

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

public class KrakenClassifier
extends ClassifierModuleImpl
implements ApiModule

This BioModule assigns taxonomy to WGS sequences and translates the results into mpa-format. Command line options are defined in the online manual: http://ccb.jhu.edu/software/kraken/MANUAL.html

GUI Module Name

Kraken Classifier

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	EXE_KRAKEN Config exe property for kraken executable: "exe.kraken"
protected static String	FUNCTION_KRAKEN Name of the kraken function used to assign taxonomy: "runKraken"
protected static String	FUNCTION_TRANSLATE Name of the translate function used to convert mpa-format to standard format: "translate"
protected static String	KRAKEN_DATABASE Config property must contain file path to Kraken kmer database directory: "kraken.db"
protected static String	KRAKEN_FILE File suffix added by BioLockJ to kraken output files (before translation): "_kraken_out.txt"
protected static String	KRAKEN_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
KrakenClassifier()

Method Summary

Modifier and Type	Method and Description
List<List<String>>	buildScript(List<File> files) Build bash script lines to classify unpaired WGS reads with Kraken.
List<List<String>>	buildScriptForPairedReads(List<File> files) Build bash script lines to classify paired WGS reads with Kraken.
void	checkDependencies() Verify that none of the derived command line parameters are included in Config."exe.kraken".
String	getCitationString() At a minimum, this should return the name and/or url for the wrapped tool.
String	getClassifierExe() Get kraken executable command: "exe.kraken"
List<String>	getClassifierParams() Obtain the kraken runtime params
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	getDetails() A extension of getDescription.
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>	getWorkerScriptFunctions() This method generates the required bash functions: "translate" and "runKraken"

Methods inherited from class biolockj.module.classifier.ClassifierModuleImpl

getClassifierType, getDbCache, getPostRequisiteModules, getSummary, setDbCache, validateModuleOrder

Methods inherited from class biolockj.module.SeqModuleImpl

getInputFiles, getSeqFiles, isValidInputModule

Methods inherited from class biolockj.module.ScriptModuleImpl

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, getFileCache, getID, getLogDir, getMenuPlacement, getMetadata, getModuleDir, getOutputDir, 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, getMenuPlacement, getPropType, getTitle, isValidProp, listProps

Methods inherited from interface biolockj.module.BioModule

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

Methods inherited from interface biolockj.module.SeqModule

getSeqFiles

Methods inherited from interface biolockj.module.ScriptModule

getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout

Field Detail

EXE_KRAKEN

protected static final String EXE_KRAKEN

Config exe property for kraken executable: "exe.kraken"

See Also:

Constant Field Values

FUNCTION_KRAKEN

protected static final String FUNCTION_KRAKEN

Name of the kraken function used to assign taxonomy: "runKraken"

See Also:

Constant Field Values

FUNCTION_TRANSLATE

protected static final String FUNCTION_TRANSLATE

Name of the translate function used to convert mpa-format to standard format: "translate"

See Also:

Constant Field Values

KRAKEN_DATABASE

protected static final String KRAKEN_DATABASE

Config property must contain file path to Kraken kmer database directory: "kraken.db"

See Also:

Constant Field Values

KRAKEN_PARAMS

protected static final String KRAKEN_PARAMS

See Also:

Constant Field Values

KRAKEN_FILE

protected static final String KRAKEN_FILE

File suffix added by BioLockJ to kraken output files (before translation): "_kraken_out.txt"

See Also:

Constant Field Values

Constructor Detail

KrakenClassifier

public KrakenClassifier()

Method Detail

buildScript

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

Build bash script lines to classify unpaired WGS reads with Kraken. The inner list contains 2 bash script lines used to classify 1 sample.

Example lines:

1. kraken --fasta-input --only-classified-output --threads 8 --db /database/kraken --output ./temp/sample42_kraken.txt ./input/sample42.fasta
   
2. kraken-translate --db /database/kraken --mpa-format ./temp/sample42_kraken.txt > ./output/sample42_reported.tsv

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

buildScriptForPairedReads

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

Build bash script lines to classify paired WGS reads with Kraken. The inner list contains 2 bash script lines used to classify 1 sample (2 files: forward and reverse reads).

Example lines:

1. kraken --paired --fasta-input --only-classified-output --threads 8 --db /database/kraken --output ./temp/sample42_kraken.txt ./input/sample42_R1.fasta ./input/sample42_R2.fasta
   
2. kraken-translate --db /database/kraken --mpa-format ./temp/sample42_kraken.txt > ./output/sample42_reported.tsv

Specified by:

buildScriptForPairedReads in interface ScriptModule

Overrides:

buildScriptForPairedReads in class ScriptModuleImpl

Parameters:

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

Returns:

Nested list of bash scripts lines

Throws:

Exception - if unable to generate the script lines

checkDependencies

public void checkDependencies()
                       throws Exception

Verify that none of the derived command line parameters are included in Config."exe.kraken".

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

Get kraken executable command: "exe.kraken"

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

Obtain the kraken runtime params

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 ConfigNotFoundException,
                  ConfigPathException,
                  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:

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

ConfigPathException - if path is defined but does not exists

DockerVolCreationException

getWorkerScriptFunctions

public List<String> getWorkerScriptFunctions()
                                      throws Exception

This method generates the required bash functions: "translate" and "runKraken"

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:

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:

getDetails

public String getDetails()

Description copied from interface: ApiModule

A extension of getDescription. Beyond the brief description, give details such as the interaction between properties.

Specified by:

getDetails in interface ApiModule

Overrides:

getDetails in class BioModuleImpl

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: