biolockj.module.seq

Class AwkFastaConverter

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.SeqModuleImpl

biolockj.module.seq.AwkFastaConverter

All Implemented Interfaces:

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

public class AwkFastaConverter
extends SeqModuleImpl
implements ApiModule

This BioModule uses awk and gzip to convert input sequence files into a decompressed fasta file format.

GUI Module Name

Awk Fastq to Fasta Converter

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	FUNCTION_CONVERT_454 Name of the bash function used to conver 454 format to BioLockJ friendly Illumina format: "convert454"
protected static String	FUNCTION_CONVERT_TO_FASTA Name of the bash function that converts the file format to Fasta: "convertToFastA"
protected static String	FUNCTION_GUNZIP Name of the bash function used to decompress gzipped files: "decompressGzip"

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
AwkFastaConverter()

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.
void	cleanUp() Set Config."internal.seqType" = "fasta" Set Config."internal.seqHeaderChar" = SeqUtil.FASTA_HEADER_DEFAULT_DELIM
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.
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.
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.
List<String>	getWorkerScriptFunctions() This method generates the required bash functions used by the module scripts.
protected static String	unzip(File file, String targetPath) Build script line to decompress gzipped sequence file.

Methods inherited from class biolockj.module.SeqModuleImpl

getInputFiles, getSummary, isValidInputModule

Methods inherited from class biolockj.module.ScriptModuleImpl

buildScriptForPairedReads, checkDependencies, executeTask, 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, 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, getMenuPlacement, getPropType, getTitle, isValidProp, listProps

Methods inherited from interface biolockj.module.BioModule

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

Methods inherited from interface biolockj.module.ScriptModule

buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout

Field Detail

FUNCTION_CONVERT_454

protected static final String FUNCTION_CONVERT_454

Name of the bash function used to conver 454 format to BioLockJ friendly Illumina format: "convert454"

See Also:

Constant Field Values

FUNCTION_CONVERT_TO_FASTA

protected static final String FUNCTION_CONVERT_TO_FASTA

Name of the bash function that converts the file format to Fasta: "convertToFastA"

See Also:

Constant Field Values

FUNCTION_GUNZIP

protected static final String FUNCTION_GUNZIP

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

See Also:

Constant Field Values

Constructor Detail

AwkFastaConverter

public AwkFastaConverter()

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

cleanUp

public void cleanUp()
             throws Exception

Set Config."internal.seqType" = "fasta"
Set Config."internal.seqHeaderChar" = SeqUtil.FASTA_HEADER_DEFAULT_DELIM

Specified by:

cleanUp in interface BioModule

Overrides:

cleanUp in class BioModuleImpl

Throws:

Exception - if errors occur

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

Overrides:

getSeqFiles in class SeqModuleImpl

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.

getWorkerScriptFunctions

public List<String> getWorkerScriptFunctions()
                                      throws Exception

This method generates the required bash functions used by the module scripts.

• "convertToFastA"
• "decompressGzip"

Specified by:

getWorkerScriptFunctions in interface ScriptModule

Overrides:

getWorkerScriptFunctions in class ScriptModuleImpl

Returns:

Bash script lines for the functions

Throws:

Exception - if errors occur

unzip

protected static String unzip(File file,
                              String targetPath)

Build script line to decompress gzipped sequence file.

Parameters:

file - Gzipped file

targetPath - Output file name

Returns:

Bash Script line to gunzip file

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:

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: