biolockj.module.implicit.parser.wgs

Class Humann2Parser

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.JavaModuleImpl

biolockj.module.implicit.parser.ParserModuleImpl

biolockj.module.implicit.parser.wgs.Humann2Parser

All Implemented Interfaces:

ApiModule, BioModule, ParserModule, JavaModule, ScriptModule, Comparable<BioModule>

public class Humann2Parser
extends ParserModuleImpl
implements ApiModule

This BioModule parses Humann2Classifier output reports to build standard OTU abundance tables.
Samples IDs are found in the column headers starting with the 2nd column.
The count type depends on the HumanN2 config properties.

GUI Module Name

HumanN2 Parser

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	HN2_KEEP_UNINTEGRATED Config Boolean property: "humann2.keepUnintegrated"
protected static String	HN2_KEEP_UNMAPPED Config Boolean property: "humann2.keepUnmapped"

Fields inherited from class biolockj.module.implicit.parser.ParserModuleImpl

NUM_OTUS

Fields inherited from class biolockj.module.JavaModuleImpl

BLJ_OPTIONS

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
Humann2Parser()

Method Summary

Modifier and Type	Method and Description
void	checkDependencies() Execute ParserModuleImpl.validateModuleOrder() to validate module configuration order.
String	getCitationString() At a minimum, this should return the name and/or url for the wrapped tool.
String	getDescription() Briefly describe what this module does.
String	getSummary() Produce summary message with min, max, mean, and median number of reads.
boolean	isValidInputModule(BioModule module) If module is a SeqModule input must contain sequence data.
Boolean	isValidProp(String property) Tests to see if the value val is valid for property prop; primarily tests format.
void	parseSamples() To parse the taxonomy level reports output by Humann2Classifier.
void	runModule() Parsers execute a task with 3 core functions: ParserModuleImpl.parseSamples() - generates ParsedSamples ParserModuleImpl.buildOtuCountFiles() - builds OTU tree tables from ParsedSamples

Methods inherited from class biolockj.module.implicit.parser.ParserModuleImpl

addOtuNode, addParsedSample, buildOtuCountFiles, getDepricatedOtuCountFields, getHitsPerSample, getOtuCountField, getParsedSample, getParsedSamples, getSampleIds, getUniqueOtus, isValid, setNumHitsFieldName, validateModuleOrder

Methods inherited from class biolockj.module.JavaModuleImpl

buildScript, executeTask, getDockerImageName, getDockerImageOwner, getDockerImageTag, getWorkerScriptFunctions, markStatus, moduleComplete, moduleFailed, runBioLockJ_CMD

Methods inherited from class biolockj.module.ScriptModuleImpl

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

Methods inherited from class biolockj.module.BioModuleImpl

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

Methods inherited from interface biolockj.module.BioModule

cleanUp, executeTask, getAlias, getDockerImageName, getDockerImageOwner, getDockerImageTag, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getResourceDir, getTempDir, init, setAlias, version

Methods inherited from interface biolockj.module.JavaModule

moduleComplete, moduleFailed

Methods inherited from interface biolockj.module.ScriptModule

buildScript, buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout, getWorkerScriptFunctions

Field Detail

HN2_KEEP_UNINTEGRATED

protected static final String HN2_KEEP_UNINTEGRATED

Config Boolean property: "humann2.keepUnintegrated"

See Also:

Constant Field Values

HN2_KEEP_UNMAPPED

protected static final String HN2_KEEP_UNMAPPED

Config Boolean property: "humann2.keepUnmapped"

See Also:

Constant Field Values

Constructor Detail

Humann2Parser

public Humann2Parser()

Method Detail

checkDependencies

public void checkDependencies()
                       throws Exception

Description copied from class: ParserModuleImpl

Execute ParserModuleImpl.validateModuleOrder() to validate module configuration order.

Specified by:

checkDependencies in interface BioModule

Overrides:

checkDependencies in class ParserModuleImpl

Throws:

Exception - thrown if missing or invalid dependencies are found

getSummary

public String getSummary()
                  throws Exception

Description copied from class: ParserModuleImpl

Produce summary message with min, max, mean, and median number of reads.

Specified by:

getSummary in interface BioModule

Overrides:

getSummary in class ParserModuleImpl

Returns:

Summary of BioModule execution

Throws:

Exception - if any error occurs

isValidInputModule

public boolean isValidInputModule(BioModule module)

Description copied from class: JavaModuleImpl

If module is a SeqModule input must contain sequence data.

Specified by:

isValidInputModule in interface BioModule

Overrides:

isValidInputModule in class JavaModuleImpl

Parameters:

module - BioModule that ran before the current BioModule

Returns:

boolean TRUE if the previousModule output is acceptable input for the current BioModule

parseSamples

public void parseSamples()
                  throws Exception

To parse the taxonomy level reports output by Humann2Classifier. Skip mapping of UNMAPPED and UNINTEGRATED columns Sample HumanN2 report line (head output_pAbund.tsv):
1st cell format: [Pathway_ID]:[Pathway_Descr] | g__[genus_taxa].s__[species_taxa]
Example: ARO-PWY: chorismate biosynthesis I|g__Acidaminococcus.s__Acidaminococcus_intestini #SampleID Metaphlan22_Analysis #clade_name relative_abundance coverage average_genome_length_in_the_clade estimated_number_of_reads_from_the_clade k__Bacteria|p__Bacteroidetes 14.68863 0.137144143537 4234739 580770

Specified by:

parseSamples in interface ParserModule

Specified by:

parseSamples in class ParserModuleImpl

Throws:

Exception - if error occurs while parsing classifier reports

runModule

public void runModule()
               throws Exception

Description copied from class: ParserModuleImpl

Parsers execute a task with 3 core functions:

1. ParserModuleImpl.parseSamples() - generates ParsedSamples
2. ParserModuleImpl.buildOtuCountFiles() - builds OTU tree tables from ParsedSamples

Specified by:

runModule in interface JavaModule

Overrides:

runModule in class ParserModuleImpl

Throws:

Exception - thrown if any runtime error occurs

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