biolockj.module.seq

Class KneadData

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.SeqModuleImpl

biolockj.module.seq.KneadData

All Implemented Interfaces:

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

public class KneadData
extends SeqModuleImpl
implements DatabaseModule, ApiModule

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": "kneaddata.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

LOG_DIR, MAIN_SCRIPT_PREFIX, NO_VERSION, OUTPUT_DIR, RES_DIR, TEMP_DIR

Constructor Summary

Constructors

Constructor and Description
KneadData()

Method Summary

Modifier and Type	Method and Description
List<List<String>>	buildScript(List<File> files) Return an inner list of lines to execute for each sample.
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 Start the AWS DB sync to S3 if a novel DB has been configure and "aws.copyDbToS3" is enabled
String	getCitationString() At a minimum, this should return the name and/or url for the wrapped tool.
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.
String	getDescription() Briefly describe what this module does.
String	getDockerImageName() Get the docker image to use for this module.
String	getDockerImageOwner() Get the name of the docker hub user that owns the image to use for this module.
String	getDockerImageTag() Get the version / tag to use for the docker image.
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".
Boolean	isValidProp(String property) Tests to see if the value val is valid for property prop; primarily tests format.

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

addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getDetails, getFileCache, getID, 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.api.ApiModule

getDescription, getDetails, getMenuPlacement, getPropType, getTitle, listProps

Methods inherited from interface biolockj.module.BioModule

cleanUp, executeTask, getAlias, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getPropDefault, getResourceDir, getTempDir, init, isValidInputModule, setAlias, version

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": "kneaddata.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 class: ScriptModuleImpl

Return an inner list of lines to execute for each sample. Return these as a list (outer list)

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
• Start the AWS DB sync to S3 if a novel DB has been configure and "aws.copyDbToS3" is enabled

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 ConfigPathException,
                  ConfigNotFoundException

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:

ConfigPathException - if path is defined but does not exists

ConfigNotFoundException - if DB property is undefined and the default DB is not included in the module runtime env

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

getSanatizedFile

protected File getSanatizedFile(String sampleId,
                                Boolean isRvRead)

Return sanitized sequence data file.

Parameters:

sampleId - Sample ID

isRvRead - Boolean TRUE to return the file containing reverse reads

Returns:

File with sanitized sequences

getDockerImageOwner

public String getDockerImageOwner()

Description copied from interface: BioModule

Get the name of the docker hub user that owns the image to use for this module. Docker images from docker hub are specified using this syntax: /:

Specified by:

getDockerImageOwner in interface BioModule

Overrides:

getDockerImageOwner in class BioModuleImpl

Returns:

getDockerImageName

public String getDockerImageName()

Description copied from interface: BioModule

Get the docker image to use for this module. The owner and version/tag are specificed separately; this is just the image name. Docker images from docker hub are specified using this syntax: /:

Specified by:

getDockerImageName in interface BioModule

Returns:

getDockerImageTag

public String getDockerImageTag()

Description copied from interface: BioModule

Get the version / tag to use for the docker image. Docker images from docker hub are specified using this syntax: /:

Specified by:

getDockerImageTag in interface BioModule

Overrides:

getDockerImageTag in class BioModuleImpl

Returns:

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:

isValidProp

public Boolean isValidProp(String property)
                    throws Exception

Description copied from interface: ApiModule

Tests to see if the value val is valid for property prop; primarily tests format. This is designed for individual properties. To make sure property values are compatible, use BioModule.checkDependencies(). Using switch/case or a stack of if/else is recommended. Within each case, call any/all method that is used by this module to access the value from the config file, leveraging the checks in the Config.get* methods. This method should never actually return false. If the value is not valid, it should throw an exception that includes a helpful message about whats not valid. As part of a throwable, that message is passed along to wherever the call started. Any time that "false" is actually the desired form, this method should be wrapped in a try/catch.

Specified by:

isValidProp in interface ApiModule

Overrides:

isValidProp in class ScriptModuleImpl

Returns:

true if value is recognized and good, false/Exception if it is recognized and invalid, null if prop is not recognized.

Throws:

Exception