biolockj.module.implicit.qiime

Class BuildQiimeMapping

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.SeqModuleImpl

biolockj.module.implicit.qiime.BuildQiimeMapping

All Implemented Interfaces:

BioModule, ScriptModule, SeqModule, Comparable<BioModule>

public class BuildQiimeMapping
extends SeqModuleImpl

This BioModule converts the metadata file into a tab delimited QIIME mapping file (if provided).
The QIIME mapping file is validated by calling QIIME script validate_mapping_file.py

QIIME mapping file requirements:

1. #SampleID = Required name of 1st column, holds sample unique identifiers, not nullable
2. BarcodeSequence = Required name of 2nd column, is nullable
3. LinkerPrimerSequence = Required name of 3rd column, is nullable
4. InputFileName = Column is required by add_qiime_labels.py, containing demultiplexed file names, not nullable
5. Description = Required name of last column, not nullable

Steps to convert metadata into QIIME mapping:

1. Reorder existing QIIME mapping columns, if any are out of order
2. Rename the 1st column (containing sample IDs) to the required value: #SampleID
3. Add missing QIIME mapping columns, if any are missing
4. Rename the validated mapping file to the original metadata file name and save to the module output directory.

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	FUNCTION_REORDER_FIELDS Name of the bash function that reorders metadata columns: "reorderColumns"
protected static String	QIIME_COMMENT Comment used to populate "Description" column
protected static String	QIIME_ID QIIME mapping file required 1st column name, containing the sample ID
protected static String	SCRIPT_VALIDATE_MAPPING QIIME script used to validate the QIIME mapping file format
protected static String	VALIDATED_MAPPING Suffix appended to the validate QIIME mapping file output to temp/mapping dir by bash script

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
BuildQiimeMapping()

Method Summary

Modifier and Type	Method and Description
File	addMissingFields() Create QIIME mapping based on metadata file, output to temp dir.
List<List<String>>	buildScript(List<File> files) Create the Qiime corrected mapping file by building a new metadata file with ordered columns, and verify the format via the "validate_mapping_file.py" script.
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.
String	getSummary() Message summarizes contents of scriptDir, and status of the QIIME mapping files (exists or not).
List<String>	getWorkerScriptFunctions() This method generates the bash function used to reorder columns as per QIIME requirements: "reorderColumns"

Methods inherited from class biolockj.module.SeqModuleImpl

getInputFiles, getSeqFiles, 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, cleanUp, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getDetails, 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.module.ScriptModule

buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout

Methods inherited from interface biolockj.module.BioModule

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

Field Detail

FUNCTION_REORDER_FIELDS

protected static final String FUNCTION_REORDER_FIELDS

Name of the bash function that reorders metadata columns: "reorderColumns"

See Also:

Constant Field Values

QIIME_COMMENT

protected static final String QIIME_COMMENT

Comment used to populate "Description" column

See Also:

Constant Field Values

QIIME_ID

protected static final String QIIME_ID

QIIME mapping file required 1st column name, containing the sample ID

See Also:

Constant Field Values

SCRIPT_VALIDATE_MAPPING

protected static final String SCRIPT_VALIDATE_MAPPING

QIIME script used to validate the QIIME mapping file format

See Also:

Constant Field Values

VALIDATED_MAPPING

protected static final String VALIDATED_MAPPING

Suffix appended to the validate QIIME mapping file output to temp/mapping dir by bash script

See Also:

Constant Field Values

Constructor Detail

BuildQiimeMapping

public BuildQiimeMapping()

Method Detail

addMissingFields

public File addMissingFields()
                      throws Exception

Create QIIME mapping based on metadata file, output to temp dir. Add required fields if missing.

Returns:

New Metadata file

Throws:

Exception - if unable to build the mapping file

buildScript

public List<List<String>> buildScript(List<File> files)
                               throws Exception

Create the Qiime corrected mapping file by building a new metadata file with ordered columns, and verify the format via the "validate_mapping_file.py" script.

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

getSummary

public String getSummary()
                  throws Exception

Message summarizes contents of scriptDir, and status of the QIIME mapping files (exists or not).

Specified by:

getSummary in interface BioModule

Overrides:

getSummary in class SeqModuleImpl

Returns:

Summary of BioModule execution

Throws:

Exception - if any error occurs

getWorkerScriptFunctions

public List<String> getWorkerScriptFunctions()
                                      throws Exception

This method generates the bash function used to reorder columns as per QIIME requirements: "reorderColumns"

Specified by:

getWorkerScriptFunctions in interface ScriptModule

Overrides:

getWorkerScriptFunctions in class ScriptModuleImpl

Returns:

Bash script lines for the functions

Throws:

Exception - if errors occur

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: /:

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: