biolockj.util

Class PathwayUtil

java.lang.Object

biolockj.util.PathwayUtil

public class PathwayUtil
extends Object

This utility helps work HumanN2 pathway abundance data.

Method Summary

Modifier and Type	Method and Description
static boolean	containsHn2ParserOutput(Collection<File> files) Check pipeline input contains Humann2Parser module output.
static String	getHn2ClassifierOutput(String type) Humann2 classifier outputs 3 types of files: "pAbund" "pCovg" "geneFam" Given the type, this method retuns the output file name.
static String	getHn2Type(File file) Humann2 classifier outputs 3 types of files: "pAbund" "pCovg" "geneFam" This method returns the type included in the given file name.
static File	getPathwayCountFile(File dir, File hn2OutputFile, String prefix) Return a pathway abundance file path in the given dir with the given prefix (if provided).
static boolean	isPathwayFile(File file) Check the file name to determine if it is a pathway abundance table file.
static boolean	isPathwayModule(BioModule module) Check the module to determine if it generated OTU count files.
static Boolean	useHumann2RawCount(BioModule module) Determine if humann2 provided most recent raw count data, used to determine getPreReq modules.
static void	verifyConfig(BioModule module) Verify the HumanN2 Config contains at least one of the following reports are enabled: "humann2.disableGeneFamilies" "humann2.disablePathCoverage" "humann2.disableGeneFamilies"

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

containsHn2ParserOutput

public static boolean containsHn2ParserOutput(Collection<File> files)

Check pipeline input contains Humann2Parser module output.

Parameters:

files - Files to test

Returns:

TRUE if pipeline input contains module input

getHn2ClassifierOutput

public static String getHn2ClassifierOutput(String type)

Humann2 classifier outputs 3 types of files:

• "pAbund"
• "pCovg"
• "geneFam"

Given the type, this method retuns the output file name.

Parameters:

type - Humann2 classifier output type

Returns:

Name of humann2 output file of the given type

getHn2Type

public static String getHn2Type(File file)
                         throws ConfigViolationException

Humann2 classifier outputs 3 types of files:

• "pAbund"
• "pCovg"
• "geneFam"

This method returns the type included in the given file name.

Parameters:

file - Humann2 classifier output type

Returns:

Name of humann2 output file of the given type

Throws:

ConfigViolationException - if unable to match the given file with a valid HN2 file type

getPathwayCountFile

public static File getPathwayCountFile(File dir,
                                       File hn2OutputFile,
                                       String prefix)
                                throws ConfigViolationException

Return a pathway abundance file path in the given dir with the given prefix (if provided).

Parameters:

dir - Directory for pathway file

hn2OutputFile - Root file indicates type of coverage, abundance, or gene

prefix - Optional prefix

Returns:

Pathway count file

Throws:

ConfigViolationException - if invalid file format detected

isPathwayFile

public static boolean isPathwayFile(File file)

Check the file name to determine if it is a pathway abundance table file.

Parameters:

file - File to test

Returns:

boolean TRUE if file is a pathway abundance file

isPathwayModule

public static boolean isPathwayModule(BioModule module)

Check the module to determine if it generated OTU count files.

Parameters:

module - BioModule

Returns:

TRUE if module generated OTU count files

useHumann2RawCount

public static Boolean useHumann2RawCount(BioModule module)
                                  throws Exception

Determine if humann2 provided most recent raw count data, used to determine getPreReq modules.

Parameters:

module - BioModule

Returns:

TRUE if humann2 counts should be used

Throws:

Exception - if errors occur

verifyConfig

public static void verifyConfig(BioModule module)
                         throws Exception

Verify the HumanN2 Config contains at least one of the following reports are enabled:

• "humann2.disableGeneFamilies"
• "humann2.disablePathCoverage"
• "humann2.disableGeneFamilies"

Parameters:

module - HumanN2 module

Throws:

Exception - if errors occur