biolockj.module.seq

Class SeqFileValidator

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.JavaModuleImpl

biolockj.module.seq.SeqFileValidator

All Implemented Interfaces:

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

public class SeqFileValidator
extends JavaModuleImpl
implements SeqModule

This BioModule validates fasta/fastq file formats are valid and enforces min/max read lengths.

GUI Module Name

Sequence File Validator

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	INPUT_SEQ_MAX Config Integer property "seqFileValidator.seqMaxLen" defines the maximum number of bases per read
protected static String	INPUT_SEQ_MIN Config Integer property "seqFileValidator.seqMinLen" defines the minimum number of bases per read
static String	NUM_VALID_READS Column name that holds number of valid reads per sample: "Num_Valid_Reads"
protected static String	REQUIRE_EUQL_NUM_PAIRS Config Boolean property "seqFileValidator.requireEqualNumPairs" determines if module requires equal number of forward and reverse reads (simple check).

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.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
SeqFileValidator()

Method Summary

Modifier and Type	Method and Description
void	cleanUp() Set "Num_Valid_Reads" as the number of reads field.
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 of valid reads containing a barcode defined in the metadata file.
protected void	removeBadFiles() Remove sequence files in which all reads failed validation checks, leaving only an empty file.
void	runModule() Cache sampleIds to compare to validated sampleIds post-processing.
protected void	validateFile(File file, Integer fileCount) Validate sequence files: Validate valid 1st sequence header character is expected character Validate fastq files have same number of bases and quality scores per read Remove reads below minimum threshold: "seqFileValidator.seqMinLen" Trim reads if above the maximum threshold: "seqFileValidator.seqMaxLen" Invalid reads are saved to a file in the module temp directory for analysis/review.
protected void	verifyPairedSeqs() Verify equal number of forward and reverse read files. if "seqFileValidator.requireEqualNumPairs"="Y", verify forward and reverse read files have an equal number of reads.

Methods inherited from class biolockj.module.JavaModuleImpl

buildScript, executeTask, getSource, getWorkerScriptFunctions, isValidInputModule, markStatus, moduleComplete, moduleFailed

Methods inherited from class biolockj.module.ScriptModuleImpl

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

Methods inherited from class biolockj.module.BioModuleImpl

cacheInputFiles, compareTo, equals, findModuleInputFiles, getFileCache, getID, getInputFiles, 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

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

Methods inherited from interface biolockj.module.BioModule

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

Field Detail

NUM_VALID_READS

public static final String NUM_VALID_READS

Column name that holds number of valid reads per sample: "Num_Valid_Reads"

See Also:

Constant Field Values

INPUT_SEQ_MAX

protected static final String INPUT_SEQ_MAX

Config Integer property "seqFileValidator.seqMaxLen" defines the maximum number of bases per read

See Also:

Constant Field Values

INPUT_SEQ_MIN

protected static final String INPUT_SEQ_MIN

Config Integer property "seqFileValidator.seqMinLen" defines the minimum number of bases per read

See Also:

Constant Field Values

REQUIRE_EUQL_NUM_PAIRS

protected static final String REQUIRE_EUQL_NUM_PAIRS

Config Boolean property "seqFileValidator.requireEqualNumPairs" determines if module requires equal number of forward and reverse reads (simple check).

See Also:

Constant Field Values

Constructor Detail

SeqFileValidator

public SeqFileValidator()

Method Detail

cleanUp

public void cleanUp()
             throws Exception

Set "Num_Valid_Reads" as the number of reads field.

Specified by:

cleanUp in interface BioModule

Overrides:

cleanUp in class BioModuleImpl

Throws:

Exception - thrown if any runtime error occurs

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

Parameters:

files - Module input files

Returns:

Module sequence files

Throws:

Exception - if no input files are found

getSummary

public String getSummary()
                  throws Exception

Produce a summary message with counts on total number of reads and number of valid reads containing a barcode defined in the metadata file.

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

Cache sampleIds to compare to validated sampleIds post-processing. Call validateFile(File, Integer) for each input file.
Call removeBadFiles() to remove empty files (cases where all reads fail validation).
Call verifyPairedSeqs() if module input files are paired read files.
Call MetaUtil.addColumn(String, Map, File, boolean)

Specified by:

runModule in interface JavaModule

Specified by:

runModule in class JavaModuleImpl

Throws:

Exception - thrown if any runtime error occurs

removeBadFiles

protected void removeBadFiles()
                       throws Exception

Remove sequence files in which all reads failed validation checks, leaving only an empty file.

Throws:

Exception - if errors occur

validateFile

protected void validateFile(File file,
                            Integer fileCount)
                     throws Exception

Validate sequence files:

1. Validate valid 1st sequence header character is expected character
2. Validate fastq files have same number of bases and quality scores per read
3. Remove reads below minimum threshold: "seqFileValidator.seqMinLen"
4. Trim reads if above the maximum threshold: "seqFileValidator.seqMaxLen"

Invalid reads are saved to a file in the module temp directory for analysis/review.

Parameters:

file - Sequence file

fileCount - Integer count

Throws:

Exception - if I/O errors occur while processing sequence files

verifyPairedSeqs

protected void verifyPairedSeqs()
                         throws Exception

Verify equal number of forward and reverse read files.
if "seqFileValidator.requireEqualNumPairs"="Y", verify forward and reverse read files have an equal number of reads.

Throws:

Exception - if validations fail or errors occur