biolockj.module.seq

Class AwkFastaConverter

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.SeqModuleImpl

biolockj.module.seq.AwkFastaConverter

All Implemented Interfaces:

BioModule, ScriptModule, SeqModule, Comparable<BioModule>

public class AwkFastaConverter
extends SeqModuleImpl

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.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
AwkFastaConverter()

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.
void	cleanUp() Set Config."internal.seqType" = "fasta" Set Config."internal.seqHeaderChar" = SeqUtil.FASTA_HEADER_DEFAULT_DELIM
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

Methods inherited from class biolockj.module.BioModuleImpl

cacheInputFiles, 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.ScriptModule

buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout

Methods inherited from interface biolockj.module.BioModule

checkDependencies, executeTask, getID, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getTempDir, init

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 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

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 Exception

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:

Exception - if no input files are found

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