biolockj.module.classifier.wgs

Class Humann2Classifier

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.SeqModuleImpl

biolockj.module.classifier.ClassifierModuleImpl

biolockj.module.classifier.wgs.Humann2Classifier

All Implemented Interfaces:

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

public class Humann2Classifier
extends ClassifierModuleImpl
implements ApiModule

This BioModule runs biobakery humann2 program to generate the HMP Unified Metabolic Analysis Network
HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question "What are the microbes in my community-of-interest doing (or capable of doing)? For more information, please review the BioBakery instruction manual: https://bitbucket.org/biobakery/humann2

GUI Module Name

HumanN2 Classifier

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	EXE_HUMANN2 Config "executable" property for humnan2 executable: "exe.humann2"
protected static String	EXE_HUMANN2_JOIN_PARAMS Config "list" property: "humann2.humann2JoinTableParams"
protected static String	EXE_HUMANN2_PARAMS Config "list" property: "humann2.humann2Params"
protected static String	EXE_HUMANN2_RENORM_PARAMS Config "list" property: "humann2.humann2RenormTableParams"
protected static String	HN2_NUCL_DB Config "file path" property: "humann2.nuclDB"
protected static String	HN2_PROT_DB Config "file path" property: "humann2.protDB"

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
Humann2Classifier()

Method Summary

Modifier and Type	Method and Description
List<List<String>>	buildScript(List<File> files) Return an inner list of lines to execute for each sample.
List<List<String>>	buildScriptForPairedReads(List<File> files) The default behavior is the same for paired or unpaired data.
void	checkDependencies() Verify that none of the derived command line parameters are included in Config."exe.humann2".
void	cleanUp() If metadata exists in module output directory, refresh MetaUtil.
void	executeTask() Calling super to build scripts, then wait until any database downloads are complete before allowing the Pipeline to move forward and use these DB.
String	getCitationString() At a minimum, this should return the name and/or url for the wrapped tool.
String	getClassifierExe() Get HumanN2 executable command: "exe.humann2"
List<String>	getClassifierParams() Obtain the humann2 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	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.
protected String	getRuntimeParams() Get formatted runtime parameters and
String	getSummary() Add database info if module is a DatabaseModule
String	getTitle() Get a human readable name for this module.
List<String>	getWorkerScriptFunctions() Method returns bash script lines used to build the functions called by the worker scripts.
Boolean	isValidProp(String property) Tests to see if the value val is valid for property prop; primarily tests format.

Methods inherited from class biolockj.module.classifier.ClassifierModuleImpl

getClassifierType, getDbCache, getPostRequisiteModules, setDbCache, validateModuleOrder

Methods inherited from class biolockj.module.SeqModuleImpl

getInputFiles, getSeqFiles, isValidInputModule

Methods inherited from class biolockj.module.ScriptModuleImpl

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

Methods inherited from class biolockj.module.BioModuleImpl

addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getDetails, getFileCache, getID, getLogDir, getMenuPlacement, getMetadata, getModuleDir, getOutputDir, getPreRequisiteModules, getPropDefault, getPropDescMap, getPropType, getPropTypeMap, getResourceDir, getTempDir, 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, listProps

Methods inherited from interface biolockj.module.BioModule

getAlias, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getResourceDir, 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_HUMANN2

protected static final String EXE_HUMANN2

Config "executable" property for humnan2 executable: "exe.humann2"

See Also:

Constant Field Values

EXE_HUMANN2_JOIN_PARAMS

protected static final String EXE_HUMANN2_JOIN_PARAMS

Config "list" property: "humann2.humann2JoinTableParams"

See Also:

Constant Field Values

EXE_HUMANN2_PARAMS

protected static final String EXE_HUMANN2_PARAMS

Config "list" property: "humann2.humann2Params"

See Also:

Constant Field Values

EXE_HUMANN2_RENORM_PARAMS

protected static final String EXE_HUMANN2_RENORM_PARAMS

Config "list" property: "humann2.humann2RenormTableParams"

See Also:

Constant Field Values

HN2_NUCL_DB

protected static final String HN2_NUCL_DB

Config "file path" property: "humann2.nuclDB"

See Also:

Constant Field Values

HN2_PROT_DB

protected static final String HN2_PROT_DB

Config "file path" property: "humann2.protDB"

See Also:

Constant Field Values

Constructor Detail

Humann2Classifier

public Humann2Classifier()

Method Detail

buildScript

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

Description copied from class: ScriptModuleImpl

Return an inner list of lines to execute for each sample. Return these as a list (outer list)

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

Description copied from class: ScriptModuleImpl

The default behavior is the same for paired or unpaired data. This method must be overridden to create separate scripts for paired datasets.

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.humann2". Also verify:

• Config."humann2.nuclDB" is a valid directory
• Config."humann2.protDB" is a valid directory

Specified by:

checkDependencies in interface BioModule

Overrides:

checkDependencies in class ClassifierModuleImpl

Throws:

Exception - thrown if missing or invalid dependencies are found

cleanUp

public void cleanUp()
             throws Exception

Description copied from class: BioModuleImpl

If metadata exists in module output directory, refresh MetaUtil.

Specified by:

cleanUp in interface BioModule

Overrides:

cleanUp in class BioModuleImpl

Throws:

Exception - thrown if any runtime error occurs

executeTask

public void executeTask()
                 throws Exception

Calling super to build scripts, then wait until any database downloads are complete before allowing the Pipeline to move forward and use these DB.

Specified by:

executeTask in interface BioModule

Overrides:

executeTask in class ScriptModuleImpl

Throws:

Exception - thrown if the module is unable to complete is task

getClassifierExe

public String getClassifierExe()
                        throws ConfigException

Get HumanN2 executable command: "exe.humann2"

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 humann2 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

getSummary

public String getSummary()
                  throws Exception

Description copied from class: SeqModuleImpl

Add database info if module is a DatabaseModule

Specified by:

getSummary in interface BioModule

Overrides:

getSummary in class ClassifierModuleImpl

Returns:

Summary of BioModule execution

Throws:

Exception - if any error occurs

getWorkerScriptFunctions

public List<String> getWorkerScriptFunctions()
                                      throws Exception

Description copied from interface: ScriptModule

Method returns bash script lines used to build the functions called by the worker scripts.

Specified by:

getWorkerScriptFunctions in interface ScriptModule

Overrides:

getWorkerScriptFunctions in class ScriptModuleImpl

Returns:

Bash script lines for the functions

Throws:

Exception - if errors occur

getRuntimeParams

protected String getRuntimeParams()
                           throws Exception

Get formatted runtime parameters and

Returns:

Formatted runtime switches

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:

getTitle

public String getTitle()

Description copied from interface: ApiModule

Get a human readable name for this module.

Specified by:

getTitle in interface ApiModule

Overrides:

getTitle 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:

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:

isValidProp

public Boolean isValidProp(String property)
                    throws Exception

Description copied from interface: ApiModule

Tests to see if the value val is valid for property prop; primarily tests format. This is designed for individual properties. To make sure property values are compatible, use BioModule.checkDependencies(). Using switch/case or a stack of if/else is recommended. Within each case, call any/all method that is used by this module to access the value from the config file, leveraging the checks in the Config.get* methods. This method should never actually return false. If the value is not valid, it should throw an exception that includes a helpful message about whats not valid. As part of a throwable, that message is passed along to wherever the call started. Any time that "false" is actually the desired form, this method should be wrapped in a try/catch.

Specified by:

isValidProp in interface ApiModule

Overrides:

isValidProp in class ScriptModuleImpl

Returns:

true if value is recognized and good, false/Exception if it is recognized and invalid, null if prop is not recognized.

Throws:

Exception