biolockj.module.classifier.r16s

Class QiimeClosedRefClassifier

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.QiimeClosedRefClassifier

All Implemented Interfaces:

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

public class QiimeClosedRefClassifier
extends QiimeClassifier
implements ApiModule

This BioModule executes the QIIME script pick_closed_reference_otus.py on a FastA sequence files. Unlike open and de novo OTU picking scripts, which require a single multiplexed file for cluster analysis, closed reference OTU picking can be run in batches (output/batch_0, output/batch_1, output/batch_2, etc.). The program awk is used to split the metadata into separate batch-specific QIIME mapping files.

GUI Module Name

QIIME Closed Reference Classifier

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	BATCH_MAPPING Name of each batch mapping file (each in its own batch directory)
protected static String	FUNCTION_CREATE_BATCH_MAPPING Name of the bash function that prepares a batch of seqs for processing: "createBatchMapping"
static String	PICK_OTU_SCRIPT Closed reference OTU picking script: "pick_closed_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
QiimeClosedRefClassifier()

Method Summary

Modifier and Type	Method and Description
List<List<String>>	buildScript(List<File> files) Create bash script lines to split up the QIIME mapping and fasta files into batches of size Config."script.numWorkers"
void	checkDependencies() Call QiimeClassifier checkOtuPickingDependencies() method to verify OTU picking script parameters.
protected String	copyBatchOtuTableToOutputDir(File batchDir, Integer batchNum) The method returns 1 bash script line that will copy the batch "otu_table.biom" from the batchDir to the output directory.
void	executeTask() Build the nested list of bash script lines that will be used by BashScriptBuilder to build the worker scripts.
protected List<String>	getBatch(List<String> lines, int batchNum, int index) Method returns batch script lines for one batch.
protected File	getBatchDir(int batchNum) Get the pipeline/module/temp/batch_# dir.
protected File	getBatchFastaDir(int batchNum) Get the pipeline/module/temp/batch_#/fasta directory.
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.
List<String>	getPostRequisiteModules() If paired reads found, return prerequisite module: PearMergeReads.
List<String>	getWorkerScriptFunctions() Method returns bash script lines used to build the functions called by the worker scripts.

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

buildQiimeDockerConfigLines, cleanUp, getClassifierExe, getClassifierParams, getDB, getDockerImageName, getDockerImageOwner, getDockerImageTag, getInputFileDir, getInputFiles, getParams, getPickOtuLines, getPreRequisiteModules, getSummary, getVsearchParams, 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, 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, getAlias, getDockerImageName, getDockerImageOwner, getDockerImageTag, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, 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

Closed reference OTU picking script: "pick_closed_reference_otus.py"

See Also:

Constant Field Values

BATCH_MAPPING

protected static final String BATCH_MAPPING

Name of each batch mapping file (each in its own batch directory)

See Also:

Constant Field Values

FUNCTION_CREATE_BATCH_MAPPING

protected static final String FUNCTION_CREATE_BATCH_MAPPING

Name of the bash function that prepares a batch of seqs for processing: "createBatchMapping"

See Also:

Constant Field Values

Constructor Detail

QiimeClosedRefClassifier

public QiimeClosedRefClassifier()

Method Detail

buildScript

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

Create bash script lines to split up the QIIME mapping and fasta files into batches of size Config."script.numWorkers"

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.

Specified by:

checkDependencies in interface BioModule

Overrides:

checkDependencies in class QiimeClassifier

Throws:

Exception - thrown if missing or invalid dependencies are found

executeTask

public void executeTask()
                 throws Exception

Build the nested list of bash script lines that will be used by BashScriptBuilder to build the worker scripts. PassQiimeClassifier.getInputFiles() to either buildScript(List) or ScriptModuleImpl.buildScriptForPairedReads(List) based on Config."internal.pairedReads". Each worker script is already written as a batch, so each batch = 1 worker script.

Specified by:

executeTask in interface BioModule

Overrides:

executeTask in class ScriptModuleImpl

Throws:

Exception - thrown if the module is unable to complete is task

getPostRequisiteModules

public List<String> getPostRequisiteModules()
                                     throws Exception

If paired reads found, return prerequisite module: PearMergeReads.

Specified by:

getPostRequisiteModules in interface BioModule

Overrides:

getPostRequisiteModules in class QiimeClassifier

Returns:

List of BioModules

Throws:

Exception - if invalid Class names are returned as post-requisites

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 QiimeClassifier

Returns:

Bash script lines for the functions

Throws:

Exception - if errors occur

copyBatchOtuTableToOutputDir

protected String copyBatchOtuTableToOutputDir(File batchDir,
                                              Integer batchNum)

The method returns 1 bash script line that will copy the batch "otu_table.biom" from the batchDir to the output directory.

Parameters:

batchDir - Batch directory

batchNum - Batch number used to name biom file, or null if processing 1 batch

Returns:

Bash script line to copy temp/otu_table.biom to output/otu_table.biom

getBatch

protected List<String> getBatch(List<String> lines,
                                int batchNum,
                                int index)
                         throws ConfigException

Method returns batch script lines for one batch.

Parameters:

lines - Batch script lines to copy fasta to batch_#/fasta

batchNum - Batch number

index - Start index used to break up mapping file

Returns:

List of batch script lines used to process batch

Throws:

ConfigException - if error occurs batching samples for worker scripts

getBatchDir

protected File getBatchDir(int batchNum)

Get the pipeline/module/temp/batch_# dir. Create it if it doesn't exist.

Parameters:

batchNum - Batch number

Returns:

Batch temp/batch_# directory

getBatchFastaDir

protected File getBatchFastaDir(int batchNum)

Get the pipeline/module/temp/batch_#/fasta directory. Create it if it doesn't exist.

Parameters:

batchNum - Batch number

Returns:

Batch temp/batch_#/fasta directory

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: