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:

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

public class Humann2Classifier
extends ClassifierModuleImpl

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 exe property for humnan2 executable: "exe.humann2"
protected static String	EXE_HUMANN2_JOIN_PARAMS Config List property used to obtain the humann2_join_tables executable params
protected static String	EXE_HUMANN2_PARAMS Config List property used to obtain the humann2 executable params
protected static String	EXE_HUMANN2_RENORM_PARAMS Config List property used to obtain the humann2_renorm_table executable params
protected static String	HN2_NUCL_DB Config Directory property must contain the nucleotide database: "humann2.nuclDB"
protected static String	HN2_PROT_DB Config Directory property must contain the protein nucleotide database: "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.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
Humann2Classifier()

Method Summary

Modifier and Type	Method and Description
List<List<String>>	buildScript(List<File> files) Method returns a nested list of bash script lines to classify samples containing forward reads only.
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""Params".
void	cleanUp() By default, no cleanUp code is required.
String	getClassifierExe() Get kraken 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.
protected String	getRuntimeParams() Get formatted runtime parameters and
String	getSummary() Add database info if module is a DatabaseModule
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, getPostRequisiteModules, 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

Methods inherited from class biolockj.module.BioModuleImpl

cacheInputFiles, compareTo, equals, findModuleInputFiles, getFileCache, getID, getModuleDir, getOutputDir, getPreRequisiteModules, 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

getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout

Methods inherited from interface biolockj.module.BioModule

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

Field Detail

EXE_HUMANN2

protected static final String EXE_HUMANN2

Config exe 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 used to obtain the humann2_join_tables executable params

See Also:

Constant Field Values

EXE_HUMANN2_PARAMS

protected static final String EXE_HUMANN2_PARAMS

Config List property used to obtain the humann2 executable params

See Also:

Constant Field Values

EXE_HUMANN2_RENORM_PARAMS

protected static final String EXE_HUMANN2_RENORM_PARAMS

Config List property used to obtain the humann2_renorm_table executable params

See Also:

Constant Field Values

HN2_NUCL_DB

protected static final String HN2_NUCL_DB

Config Directory property must contain the nucleotide database: "humann2.nuclDB"

See Also:

Constant Field Values

HN2_PROT_DB

protected static final String HN2_PROT_DB

Config Directory property must contain the protein nucleotide database: "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 interface: ScriptModule

Method returns a nested list of bash script lines to classify samples containing forward reads only. The inner list contains the bash script lines required to classify 1 sample.

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""Params". 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

By default, no cleanUp code is required.

Specified by:

cleanUp in interface BioModule

Overrides:

cleanUp in class BioModuleImpl

Throws:

Exception - thrown if any runtime error occurs

getClassifierExe

public String getClassifierExe()
                        throws Exception

Get kraken executable command: "exe.humann2"

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

Obtain the humann2 runtime params

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

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