biolockj.module.implicit.qiime

Class MergeQiimeOtuTables

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.implicit.qiime.MergeQiimeOtuTables

All Implemented Interfaces:

BioModule, ScriptModule, Comparable<BioModule>

public class MergeQiimeOtuTables
extends ScriptModuleImpl

This BioModule will run immediately after QiimeClosedRefClassifier if multiple otu_table.biom files were created.

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	SCRIPT_MERGE_OTU_TABLES QIIME script to merge multiple OTU tables in biom format.

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
MergeQiimeOtuTables()

Method Summary

Modifier and Type	Method and Description
List<List<String>>	buildScript(List<File> files) Build a single bash script line to call "merge_otu_tables.py" to create the single "otu_table.biom", as required by QiimeParser.
void	checkDependencies() Verify the previous module = QiimeClosedRefClassifier
void	executeTask() Call buildScript(List) to create bash script lines needed to merge "otu_table.biom"s with "merge_otu_tables.py" unless only 1 input file found, in which case, just copy it to the output dir.

Methods inherited from class biolockj.module.ScriptModuleImpl

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

Methods inherited from class biolockj.module.BioModuleImpl

cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getFileCache, getID, getInputFiles, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getTempDir, init, isValidInputModule, toString, validateFileNameUnique

Methods inherited from class java.lang.Object

clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface biolockj.module.BioModule

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

Field Detail

SCRIPT_MERGE_OTU_TABLES

protected static final String SCRIPT_MERGE_OTU_TABLES

QIIME script to merge multiple OTU tables in biom format.

See Also:

Constant Field Values

Constructor Detail

MergeQiimeOtuTables

public MergeQiimeOtuTables()

Method Detail

buildScript

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

Build a single bash script line to call "merge_otu_tables.py" to create the single "otu_table.biom", as required by QiimeParser.

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

checkDependencies

public void checkDependencies()
                       throws Exception

Verify the previous module = QiimeClosedRefClassifier

Specified by:

checkDependencies in interface BioModule

Overrides:

checkDependencies in class ScriptModuleImpl

Throws:

Exception - thrown if missing or invalid dependencies are found

executeTask

public void executeTask()
                 throws Exception

Call buildScript(List) to create bash script lines needed to merge "otu_table.biom"s with "merge_otu_tables.py" unless only 1 input file found, in which case, just copy it to the output dir.

Specified by:

executeTask in interface BioModule

Overrides:

executeTask in class ScriptModuleImpl

Throws:

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