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:

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

public class Humann2Parser
extends ParserModuleImpl

This BioModules 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" Set value = "Y" to keep UNINTEGRATED column in count tables
protected static String	HN2_KEEP_UNMAPPED Config Boolean property: "humann2.keepUnmapped" Set value = "Y" to keep UNMAPPED column in count tables

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.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
Humann2Parser()

Method Summary

Modifier and Type	Method and Description
void	checkDependencies() Execute ParserModuleImpl.validateModuleOrder() to validate module configuration order.
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.
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 the ParsedSamples

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

addOtuNode, buildOtuCountFiles, getDepricatedOtuCountFields, getOtuCountField, getParsedSample, isValid, setNumHitsFieldName, validateModuleOrder

Methods inherited from class biolockj.module.JavaModuleImpl

buildScript, executeTask, getSource, getWorkerScriptFunctions, markStatus, moduleComplete, moduleFailed

Methods inherited from class biolockj.module.ScriptModuleImpl

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

Methods inherited from class biolockj.module.BioModuleImpl

cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getFileCache, getID, getInputFiles, getModuleDir, getOutputDir, getPostRequisiteModules, 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.JavaModule

moduleComplete, moduleFailed

Methods inherited from interface biolockj.module.ScriptModule

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

Methods inherited from interface biolockj.module.BioModule

cleanUp, executeTask, getID, getInputFiles, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getTempDir, init

Field Detail

HN2_KEEP_UNINTEGRATED

protected static final String HN2_KEEP_UNINTEGRATED

Config Boolean property: "humann2.keepUnintegrated"
Set value = "Y" to keep UNINTEGRATED column in count tables

See Also:

Constant Field Values

HN2_KEEP_UNMAPPED

protected static final String HN2_KEEP_UNMAPPED

Config Boolean property: "humann2.keepUnmapped"
Set value = "Y" to keep UNMAPPED column in count tables

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 the ParsedSamples

Specified by:

runModule in interface JavaModule

Overrides:

runModule in class ParserModuleImpl

Throws:

Exception - thrown if any runtime error occurs