biolockj.module.seq

Class RarefySeqs

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.JavaModuleImpl

biolockj.module.seq.RarefySeqs

All Implemented Interfaces:

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

public class RarefySeqs
extends JavaModuleImpl
implements SeqModule, ApiModule

This BioModule imposes a minimum and/or maximum number of reads per sample. Samples below the minimum are discarded. Samples above the maximum are limited by selecting random reads up to the maximum value.

GUI Module Name

Rarefy Seqs

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	INPUT_RAREFYING_MAX Config property "rarefySeqs.max" defines the maximum number of reads per file
protected static String	INPUT_RAREFYING_MIN Config property "rarefySeqs.min" defines the minimum number of reads per file
static String	NUM_RAREFIED_READS Metadata column name for column that holds number of rarefied reads per sample: "Num_Rarefied_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
RarefySeqs()

Method Summary

Modifier and Type	Method and Description
protected void	buildRarefiedFile(File input, List<Long> indexes) Build the rarefied file for the input file, keeping only the given indexes
void	checkDependencies() Validate module dependencies Validate Config.INPUT_RAREFYING_MIN is a non-negative integer Validate Config.INPUT_RAREFYING_MAX is a positive integer that is greater than or equal to Config.INPUT_RAREFYING_MIN (if defined)
void	cleanUp() Set "Num_Rarefied_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.
String	getDetails() A extension of getDescription.
List<String>	getPreRequisiteModules() This method always requires a prerequisite module with a "number of reads" count such as: RegisterNumReads.
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 summary message with min, max, mean, and median number of reads.
protected void	rarefy(File seqFile) Builds the rarefied file if too many seqs found, or adds files with too few samples to the list of bad samples.
void	runModule() For each file with number reads outside of Config.INPUT_RAREFYING_MIN and Config.INPUT_RAREFYING_MAX values, generate a new sequence file from a shuffled list of its sequences.

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, getFileCache, getID, getInputFiles, getLogDir, getMenuPlacement, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, 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, getPropDefault, getResourceDir, getTempDir, init, isValidInputModule, setAlias, version

Methods inherited from interface biolockj.api.ApiModule

getDescription, getMenuPlacement, getPropType, getTitle, isValidProp, listProps

Field Detail

NUM_RAREFIED_READS

public static final String NUM_RAREFIED_READS

Metadata column name for column that holds number of rarefied reads per sample: "Num_Rarefied_Reads"

See Also:

Constant Field Values

INPUT_RAREFYING_MAX

protected static final String INPUT_RAREFYING_MAX

Config property "rarefySeqs.max" defines the maximum number of reads per file

See Also:

Constant Field Values

INPUT_RAREFYING_MIN

protected static final String INPUT_RAREFYING_MIN

Config property "rarefySeqs.min" defines the minimum number of reads per file

See Also:

Constant Field Values

Constructor Detail

RarefySeqs

public RarefySeqs()

Method Detail

checkDependencies

public void checkDependencies()
                       throws Exception

Validate module dependencies

1. Validate Config.INPUT_RAREFYING_MIN is a non-negative integer
2. Validate Config.INPUT_RAREFYING_MAX is a positive integer that is greater than or equal to Config.INPUT_RAREFYING_MIN (if defined)

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_Rarefied_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

getPreRequisiteModules

public List<String> getPreRequisiteModules()
                                    throws Exception

This method always requires a prerequisite module with a "number of reads" count such as: RegisterNumReads. If paired reads found, also return a 2nd module: PearMergeReads.

Specified by:

getPreRequisiteModules in interface BioModule

Overrides:

getPreRequisiteModules in class BioModuleImpl

Returns:

List of BioModule Class Names

Throws:

Exception - if invalid Class names are returned as prerequisites

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

Produce summary message with min, max, mean, and median number of reads.

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

For each file with number reads outside of Config.INPUT_RAREFYING_MIN and Config.INPUT_RAREFYING_MAX values, generate a new sequence file from a shuffled list of its sequences.

Specified by:

runModule in interface JavaModule

Specified by:

runModule in class JavaModuleImpl

Throws:

Exception - thrown if any runtime error occurs

buildRarefiedFile

protected void buildRarefiedFile(File input,
                                 List<Long> indexes)
                          throws Exception

Build the rarefied file for the input file, keeping only the given indexes

Parameters:

input - Sequence file

indexes - List of indexes to keep

Throws:

Exception - if unable to build rarefied file

rarefy

protected void rarefy(File seqFile)
               throws Exception

Builds the rarefied file if too many seqs found, or adds files with too few samples to the list of bad samples.

Parameters:

seqFile - Sequence file to rarefy

Throws:

Exception - if processing errors occur

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: