biolockj.module.classifier.wgs

Class Metaphlan2Classifier

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.SeqModuleImpl

biolockj.module.classifier.ClassifierModuleImpl

biolockj.module.classifier.wgs.Metaphlan2Classifier

All Implemented Interfaces:

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

public class Metaphlan2Classifier
extends ClassifierModuleImpl
implements ApiModule

This BioModule builds the bash scripts used to execute metaphlan2.py to classify WGS sequences with MetaPhlAn2.

GUI Module Name

MetaPhlAn2 Classifier

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	EXE_METAPHLAN Config exe property used to obtain the metaphlan2 executable
protected static String	EXE_METAPHLAN_PARAMS Config List property used to obtain the metaphlan2 executable params
protected static String	METAPHLAN2_DB Config Directory property containing alternate database: "metaphlan2.db" Must always be paired with "metaphlan2.mpa_pkl"
protected static String	METAPHLAN2_MPA_PKL Config File property containing path to the mpa_pkl file used to reference an alternate DB "metaphlan2.mpa_pkl" Must always be paired with "metaphlan2.db"

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
Metaphlan2Classifier()

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 Metaphlan.
List<List<String>>	buildScriptForPairedReads(List<File> files) Build bash script lines to classify paired WGS reads with Metaphlan.
void	checkDependencies() Verify none of the derived command line parameters are included in Config."exe.metaphlan2"
String	getCitationString() At a minimum, this should return the name and/or url for the wrapped tool.
String	getClassifierExe() Metaphlan runs python scripts, so no special command is required
List<String>	getClassifierParams() Obtain the metaphlan2 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	getParams() Metaphlan queries require standard parameters: --input_type, --nproc, -t Verify no invalid runtime params are passed and add rankSwitch if needed. Set the rankSwitch based on the Config."report.taxonomyLevels" if only one taxonomy level is to be reported, otherwise report all levels.
List<String>	getWorkerScriptFunctions() Method returns bash script lines used to build the functions called by the worker scripts.

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, getDetails, 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, getDetails, 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_METAPHLAN

protected static final String EXE_METAPHLAN

Config exe property used to obtain the metaphlan2 executable

See Also:

Constant Field Values

EXE_METAPHLAN_PARAMS

protected static final String EXE_METAPHLAN_PARAMS

Config List property used to obtain the metaphlan2 executable params

See Also:

Constant Field Values

METAPHLAN2_DB

protected static final String METAPHLAN2_DB

Config Directory property containing alternate database: "metaphlan2.db"
Must always be paired with "metaphlan2.mpa_pkl"

See Also:

Constant Field Values

METAPHLAN2_MPA_PKL

protected static final String METAPHLAN2_MPA_PKL

Config File property containing path to the mpa_pkl file used to reference an alternate DB "metaphlan2.mpa_pkl"
Must always be paired with "metaphlan2.db"

See Also:

Constant Field Values

Constructor Detail

Metaphlan2Classifier

public Metaphlan2Classifier()

Method Detail

buildScript

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

Build bash script lines to classify unpaired WGS reads with Metaphlan. The inner list contains 1 bash script line per sample.

Example line:
python /app/metaphlan2.py --nproc 8 -t rel_ab_w_read_stats --input_type fasta ./input/sample42.fasta --bowtie2out ./temp/sample42.bowtie2.bz2 > ./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 Metaphlan. The inner list contains 1 bash script line per sample.

Example line:
python /app/metaphlan2.py --nproc 8 -t rel_ab_w_read_stats --input_type fasta ./input/sample42_R1.fasta, ./input/sample42_R2.fasta --bowtie2out ./temp/sample42.bowtie2.bz2 > ./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 none of the derived command line parameters are included in Config."exe.metaphlan2"

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

Metaphlan runs python scripts, 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,
                                        DockerVolCreationException

Obtain the metaphlan2 runtime params

Specified by:

getClassifierParams in interface ClassifierModule

Specified by:

getClassifierParams in class ClassifierModuleImpl

Returns:

Runtime parameters

Throws:

DockerVolCreationException

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

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

getParams

protected String getParams()
                    throws Exception

Metaphlan queries require standard parameters: --input_type, --nproc, -t
Verify no invalid runtime params are passed and add rankSwitch if needed.
Set the rankSwitch based on the Config."report.taxonomyLevels" if only one taxonomy level is to be reported, otherwise report all levels.

Returns:

runtime parameters

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:

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: