biolockj.module.seq

Class KneadData

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.SeqModuleImpl

biolockj.module.seq.KneadData

All Implemented Interfaces:

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

public class KneadData
extends SeqModuleImpl
implements DatabaseModule

This BioModule runs biobakery kneaddata program to remove contaminated DNA.
Multiple contaminent DNA databases can be used to filter reads simultaniously.
Common contaminents include Human, Viral, and Plasmid DNA.

GUI Module Name

Knead Data Sanitizer

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	EXE_KNEADDATA KneadData executable: "exe.kneaddata"
protected static String	EXE_KNEADDATA_PARAMS Config property containing parameters for "exe.kneaddata": "exe.kneaddataParams"
protected static String	FUNCTION_SANATIZE Name of the bash function used to decompress gzipped files: "sanatizeData"
protected static String	KNEAD_DBS Config required property to the contaminent databases "kneaddata.dbs":

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

MAIN_SCRIPT_PREFIX, OUTPUT_DIR, TEMP_DIR

Fields inherited from interface biolockj.module.ScriptModule

SCRIPT_BATCH_SIZE, SCRIPT_DEFAULT_HEADER, SCRIPT_NUM_THREADS, SCRIPT_PERMISSIONS, SCRIPT_TIMEOUT

Constructor Summary

Constructors

Constructor and Description
KneadData()

Method Summary

Modifier and Type	Method and Description
List<List<String>>	buildScript(List<File> files) Method returns a nested list of bash script lines to classify samples containing forward reads only.
protected List<String>	buildScriptLinesToMoveValidSeqsToOutputDir(String sampleId) Move 1 file named /"Sample_ID.fastq/" if module input consists of forward reads only. If module input contains paired reads, move 2 files named /"Sample_ID_paired_1.fastq/" and /"Sample_ID_paired_2.fastq/" to the module output directory (after renaming them to BioLockJ standards).
void	checkDependencies() Validate module dependencies: Require Config. exists Require Config. is positive integer Require Config. is positive integer Verify Config. is positive integer if set
File	getDB() Return database directory, if multiple databases are configured, they must share a common parent directory and the common parent directory is returned by this method.
protected String	getDBs() Get the configured database parameters
protected File	getSanatizedFile(String sampleId, Boolean isRvRead) Return sanitized sequence data file.
String	getSummary() Add database info if module is a DatabaseModule
List<String>	getWorkerScriptFunctions() This method generates the worker script function: "sanatizeData".

Methods inherited from class biolockj.module.SeqModuleImpl

getInputFiles, getSeqFiles, isValidInputModule

Methods inherited from class biolockj.module.ScriptModuleImpl

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

Methods inherited from class biolockj.module.BioModuleImpl

cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getFileCache, getID, 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.BioModule

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

Methods inherited from interface biolockj.module.ScriptModule

buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout

Field Detail

EXE_KNEADDATA

protected static final String EXE_KNEADDATA

KneadData executable: "exe.kneaddata"

See Also:

Constant Field Values

EXE_KNEADDATA_PARAMS

protected static final String EXE_KNEADDATA_PARAMS

Config property containing parameters for "exe.kneaddata": "exe.kneaddataParams"

See Also:

Constant Field Values

FUNCTION_SANATIZE

protected static final String FUNCTION_SANATIZE

Name of the bash function used to decompress gzipped files: "sanatizeData"

See Also:

Constant Field Values

KNEAD_DBS

protected static final String KNEAD_DBS

Config required property to the contaminent databases "kneaddata.dbs":

See Also:

Constant Field Values

Constructor Detail

KneadData

public KneadData()

Method Detail

buildScript

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

Description copied from interface: ScriptModule

Method returns a nested list of bash script lines to classify samples containing forward reads only. The inner list contains the bash script lines required to classify 1 sample.

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

Description copied from class: ScriptModuleImpl

Validate module dependencies:

• Require Config. exists
• Require Config. is positive integer
• Require Config. is positive integer
• Verify Config. is positive integer if set

Specified by:

checkDependencies in interface BioModule

Overrides:

checkDependencies in class ScriptModuleImpl

Throws:

Exception - thrown if missing or invalid dependencies are found

getDB

public File getDB()
           throws Exception

Description copied from interface: DatabaseModule

Return database directory, if multiple databases are configured, they must share a common parent directory and the common parent directory is returned by this method.

Specified by:

getDB in interface DatabaseModule

Returns:

Database directory

Throws:

Exception - thrown if any runtime error occurs

getSummary

public String getSummary()
                  throws Exception

Description copied from class: SeqModuleImpl

Add database info if module is a DatabaseModule

Specified by:

getSummary in interface BioModule

Overrides:

getSummary in class SeqModuleImpl

Returns:

Summary of BioModule execution

Throws:

Exception - if any error occurs

getWorkerScriptFunctions

public List<String> getWorkerScriptFunctions()
                                      throws Exception

This method generates the worker script function: "sanatizeData".

Specified by:

getWorkerScriptFunctions in interface ScriptModule

Overrides:

getWorkerScriptFunctions in class ScriptModuleImpl

Returns:

Bash script lines for the functions

Throws:

Exception - if errors occur

buildScriptLinesToMoveValidSeqsToOutputDir

protected List<String> buildScriptLinesToMoveValidSeqsToOutputDir(String sampleId)
                                                           throws Exception

Move 1 file named /"Sample_ID.fastq/" if module input consists of forward reads only.
If module input contains paired reads, move 2 files named /"Sample_ID_paired_1.fastq/" and /"Sample_ID_paired_2.fastq/" to the module output directory (after renaming them to BioLockJ standards).

Parameters:

sampleId - Sample ID

Returns:

Script lines to move the file or files

Throws:

Exception - if errors occur building lines

getDBs

protected String getDBs()
                 throws Exception

Get the configured database parameters

Returns:

Database parameters

Throws:

Exception - if errors occur

getSanatizedFile

protected File getSanatizedFile(String sampleId,
                                Boolean isRvRead)
                         throws Exception

Return sanitized sequence data file.

Parameters:

sampleId - Sample ID

isRvRead - Boolean TRUE to return the file containing reverse reads

Returns:

File with sanitized sequences

Throws:

Exception - if errors occur