biolockj.module.seq

Class Multiplexer

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.JavaModuleImpl

biolockj.module.seq.Multiplexer

All Implemented Interfaces:

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

public class Multiplexer
extends JavaModuleImpl
implements SeqModule, ApiModule

This BioModule will merge sequence files into a single combined sequence file, with either the sample ID or an identifying bar-code (if defined in the metatata) is stored in the sequence header.
BioLockJ is designed to run on demultiplexed data so this must be the last module to run in its branch.

GUI Module Name

Multiplexer

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	DO_GZIP Config boolean property: "multiplexer.gzip":

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
Multiplexer()

Method Summary

Modifier and Type	Method and Description
void	checkDependencies() Validate module dependencies: Validate this is the last module to run (excluding Email) If this module was completed on a previous run, update the property: Config."internal.multiplexed" = "Y"
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.
protected String	getHeader(File file, List<String> seqLines) Get the header for the sequence.
List<File>	getSeqFiles(Collection<File> files) Return only sequence files for sample IDs found in the metadata file. If Config."metadata.required" = "Y", an error is thrown to list the files that cannot be matched to a metadata row.
String	getSummary() Produce a summary message with counts on total number of reads and number reads multiplexed.
protected void	multiplex(File sample) Add file sequences to the multiplexed file.
void	runModule() Execute multiplex(File) on each input file
protected void	validateModuleOrder() This method ensures that the multiplexed data is not passed to other modules. This must be the last module, or last module before the Email.

Methods inherited from class biolockj.module.JavaModuleImpl

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

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, 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.module.ScriptModule

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

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, isValidInputModule, setAlias, version

Methods inherited from interface biolockj.api.ApiModule

getDescription, getDetails, getMenuPlacement, getPropType, getTitle, isValidProp, listProps

Field Detail

DO_GZIP

protected static final String DO_GZIP

Config boolean property: "multiplexer.gzip":

See Also:

Constant Field Values

Constructor Detail

Multiplexer

public Multiplexer()

Method Detail

checkDependencies

public void checkDependencies()
                       throws Exception

Validate module dependencies:

1. Validate this is the last module to run (excluding Email)

If this module was completed on a previous run, update the property: Config."internal.multiplexed" = "Y"

Specified by:

checkDependencies in interface BioModule

Overrides:

checkDependencies in class ScriptModuleImpl

Throws:

Exception - thrown if missing or invalid dependencies are found

getSeqFiles

public List<File> getSeqFiles(Collection<File> files)
                       throws SequnceFormatException

Description copied from interface: SeqModule

Return only sequence files for sample IDs found in the metadata file.
If Config."metadata.required" = "Y", an error is thrown to list the files that cannot be matched to a metadata row.

Specified by:

getSeqFiles in interface SeqModule

Parameters:

files - Module input files

Returns:

Module sequence files

Throws:

SequnceFormatException - If Config."metadata.required" = "Y" but sequence files found that do not have a corresponding record in the metadata file or if invalid metadata prevents parsing SEQ files.

getSummary

public String getSummary()
                  throws Exception

Produce a summary message with counts on total number of reads and number reads multiplexed.

Specified by:

getSummary in interface BioModule

Overrides:

getSummary in class ScriptModuleImpl

Returns:

Summary of BioModule execution

Throws:

Exception - if any error occurs

runModule

public void runModule()
               throws Exception

Execute multiplex(File) on each input file

Specified by:

runModule in interface JavaModule

Specified by:

runModule in class JavaModuleImpl

Throws:

Exception - thrown if any runtime error occurs

getHeader

protected String getHeader(File file,
                           List<String> seqLines)
                    throws Exception

Get the header for the sequence.

Parameters:

file - Sequence file in fasta or fastq format

seqLines - Sequence lines for 1 read

Returns:

the header row for the sequence

Throws:

Exception - if errors occur while obtaining header

multiplex

protected void multiplex(File sample)
                  throws Exception

Add file sequences to the multiplexed file. If barcode is defined in the metadata file and set in the Config file, it will be added to the header (if not already in the header line). If no barcode value is configured, the sample ID will be used in the sequence headers.

Parameters:

sample - Sequence file in Fasta or Fastq format

Throws:

Exception - if I/O errors occur creating multiplexed file

validateModuleOrder

protected void validateModuleOrder()
                            throws Exception

This method ensures that the multiplexed data is not passed to other modules.
This must be the last module, or last module before the Email.

Throws:

Exception - if not the last module before Email

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: