biolockj.module.seq

Class TrimPrimers

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.JavaModuleImpl

biolockj.module.seq.TrimPrimers

All Implemented Interfaces:

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

public class TrimPrimers
extends JavaModuleImpl
implements SeqModule, ApiModule, ReadCounter

This BioModule removes sequence primers from demultiplexed files.
The primers are defined using regular expressions in a separate file.

GUI Module Name

Trim Primers

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	INPUT_REQUIRE_PRIMER Config property "trimPrimers.requirePrimer" is a boolean used to determine if sequences without a primer should be kept or discarded
static String	INPUT_TRIM_SEQ_FILE Config property "trimPrimers.filePath" defines the file path to the file that defines the primers as regular expressions.
static String	NUM_TRIMMED_READS Metadata column name for column that holds number of trimmed reads per sample: "Num_Trimmed_Reads"

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.BioModule

LOG_DIR, MAIN_SCRIPT_PREFIX, NO_VERSION, OUTPUT_DIR, RES_DIR, TEMP_DIR

Constructor Summary

Constructors

Constructor and Description
TrimPrimers()

Method Summary

Modifier and Type	Method and Description
protected void	addBadFilesToSummary() Update summaryMsgs with list of seq files that contained no reads with a valid primer.
void	checkDependencies() Validates the file that defines the REGEX primers.
void	cleanUp() Set "Num_Trimmed_Reads" as the number of reads field.
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.
protected Set<String>	getPrimers() Get the primers listed in the .
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() Output the summary messages generated by the module.
void	runModule() Trims primers from fasta or fastq files.

Methods inherited from class biolockj.module.JavaModuleImpl

buildScript, executeTask, getDockerImageName, getDockerImageOwner, getDockerImageTag, getWorkerScriptFunctions, isValidInputModule, markStatus, moduleComplete, moduleFailed, runBioLockJ_CMD

Methods inherited from class biolockj.module.ScriptModuleImpl

buildScriptForPairedReads, 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, getDetails, getFileCache, getID, getInputFiles, 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.module.ScriptModule

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

Methods inherited from interface biolockj.module.BioModule

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

Methods inherited from interface biolockj.api.ApiModule

getDescription, getDetails, getMenuPlacement, getPropType, getTitle, isValidProp, listProps

Field Detail

NUM_TRIMMED_READS

public static final String NUM_TRIMMED_READS

Metadata column name for column that holds number of trimmed reads per sample: "Num_Trimmed_Reads"

See Also:

Constant Field Values

INPUT_TRIM_SEQ_FILE

public static final String INPUT_TRIM_SEQ_FILE

Config property "trimPrimers.filePath" defines the file path to the file that defines the primers as regular expressions.

See Also:

Constant Field Values

INPUT_REQUIRE_PRIMER

protected static final String INPUT_REQUIRE_PRIMER

Config property "trimPrimers.requirePrimer" is a boolean used to determine if sequences without a primer should be kept or discarded

See Also:

Constant Field Values

Constructor Detail

TrimPrimers

public TrimPrimers()

Method Detail

checkDependencies

public void checkDependencies()
                       throws Exception

Validates the file that defines the REGEX primers. If primers are located at start of read, add REGEX line anchor "^" to the start of the primer sequence in "trimPrimers.filePath".

• If seqs are multiplexed, Demultiplexer must run as a prerequisite module
• If seqs are paired-end reads, and PearMergeReads is configured before this module, "trimPrimers.filePath" must contain the reverse compliment of the reverse primer with a REGEX line anchor "$" at the end.

Specified by:

checkDependencies in interface BioModule

Overrides:

checkDependencies in class ScriptModuleImpl

Throws:

Exception - thrown if missing or invalid dependencies are found

cleanUp

public void cleanUp()
             throws Exception

Set "Num_Trimmed_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 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

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.

getSummary

public String getSummary()
                  throws Exception

Output the summary messages generated by the module.

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

Trims primers from fasta or fastq files. Saves messages for summary email with metrics on best/worst and average files. Just a quick implementation on reporting metrics is working but code needs clean-up and simplification.

Specified by:

runModule in interface JavaModule

Specified by:

runModule in class JavaModuleImpl

Throws:

Exception - thrown if any runtime error occurs

addBadFilesToSummary

protected void addBadFilesToSummary()

Update summaryMsgs with list of seq files that contained no reads with a valid primer.

getPrimers

protected Set<String> getPrimers()
                          throws Exception

Get the primers listed in the . If a merged fw primer (starting with ^) and a merged rv primer (ending with $) are found set mergedReadTwoPrimers = true to enforce reads must have both primers if discarding reads without valid primers

Returns:

Set of primers

Throws:

Exception - if unable to read the file

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: