biolockj.module.classifier.r16s

Class QiimeOpenRefClassifier

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.SeqModuleImpl

biolockj.module.classifier.ClassifierModuleImpl

biolockj.module.implicit.qiime.QiimeClassifier

biolockj.module.classifier.r16s.QiimeOpenRefClassifier

All Implemented Interfaces:

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

public class QiimeOpenRefClassifier
extends QiimeClassifier
implements ApiModule

This module runs the QIIME pick_open_reference_otus.py script on FastA sequence files in a single script so it is important to allocate sufficient job resources if running in a clustered environment.

GUI Module Name

QIIME Open Reference Classifier

Field Summary

Fields

Modifier and Type	Field and Description
static String	PICK_OTU_SCRIPT Open reference OTU picking script: "pick_open_reference_otus.py"

Fields inherited from class biolockj.module.implicit.qiime.QiimeClassifier

ALPHA_DIV_NULL_VALUE, ALPHA_DIVERSITY_TABLE, CITE_QIIME, COMBINED_FNA, EXE_VSEARCH, EXE_VSEARCH_PARAMS, OTU_SUMMARY_FILE, OTU_TABLE, QIIME_PARAMS, QIIME_PYNAST_ALIGN_DB, QIIME_REF_SEQ_DB, QIIME_REMOVE_CHIMERAS, QIIME_TAXA_DB, REP_SET, SCRIPT_ADD_ALPHA_DIVERSITY, SCRIPT_ADD_LABELS, SCRIPT_CALC_ALPHA_DIVERSITY, SCRIPT_FILTER_OTUS, SCRIPT_PRINT_CONFIG, SCRIPT_SUMMARIZE_BIOM, SCRIPT_SUMMARIZE_TAXA, SUMMARIZE_TAXA_SUPPRESS_BIOM

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
QiimeOpenRefClassifier()

Method Summary

Modifier and Type	Method and Description
List<List<String>>	buildScript(List<File> files) Return bash script lines to pick open reference OTUs by passing the newest biom file in the temp directory [via bash code "$(ls -t $tempDir/*.biom | head -1)"] to QiimeClassifier getPickOtuLines() method.
void	checkDependencies() Call QiimeClassifier checkOtuPickingDependencies() method to verify OTU picking script parameters.
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	getDetails() A extension of getDescription.

Methods inherited from class biolockj.module.implicit.qiime.QiimeClassifier

buildQiimeDockerConfigLines, cleanUp, getClassifierExe, getClassifierParams, getDB, getDockerImageName, getDockerImageOwner, getDockerImageTag, getInputFileDir, getInputFiles, getParams, getPickOtuLines, getPostRequisiteModules, getPreRequisiteModules, getSummary, getVsearchParams, getWorkerScriptFunctions, isValidInputModule

Methods inherited from class biolockj.module.classifier.ClassifierModuleImpl

getClassifierType, getDbCache, setDbCache, validateModuleOrder

Methods inherited from class biolockj.module.SeqModuleImpl

getSeqFiles

Methods inherited from class biolockj.module.ScriptModuleImpl

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

Methods inherited from class biolockj.module.BioModuleImpl

addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getFileCache, getID, getLogDir, getMenuPlacement, getMetadata, getModuleDir, getOutputDir, 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, getMenuPlacement, getPropType, getTitle, isValidProp, listProps

Methods inherited from interface biolockj.module.BioModule

cleanUp, executeTask, getAlias, getDockerImageName, getDockerImageOwner, getDockerImageTag, 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

buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout

Field Detail

PICK_OTU_SCRIPT

public static final String PICK_OTU_SCRIPT

Open reference OTU picking script: "pick_open_reference_otus.py"

See Also:

Constant Field Values

Constructor Detail

QiimeOpenRefClassifier

public QiimeOpenRefClassifier()

Method Detail

buildScript

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

Return bash script lines to pick open reference OTUs by passing the newest biom file in the temp directory [via bash code "$(ls -t $tempDir/*.biom | head -1)"] to QiimeClassifier getPickOtuLines() method.

Several biom files are generated by this script, the script will select biomFile =
If property "qiime.removeChimeras" = "Y", use vsearch to identify chimeras and call "filter_otus_from_otu_table.py" to remove them from "otu_table.biom"

Specified by:

buildScript in interface ScriptModule

Overrides:

buildScript in class QiimeClassifier

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

checkDependencies

public void checkDependencies()
                       throws Exception

Call QiimeClassifier checkOtuPickingDependencies() method to verify OTU picking script parameters. If not in Docker mode and property "qiime.removeChimeras" = "Y", verify "qiime.vsearchParams".

Specified by:

checkDependencies in interface BioModule

Overrides:

checkDependencies in class QiimeClassifier

Throws:

Exception - thrown if missing or invalid dependencies are found

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:

getDetails

public String getDetails()

Description copied from interface: ApiModule

A extension of getDescription. Beyond the brief description, give details such as the interaction between properties.

Specified by:

getDetails in interface ApiModule

Overrides:

getDetails in class BioModuleImpl

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: