Package org.snpeff.snpEffect.commandLine

Class SnpEffCmdGsa

java.lang.Object

org.snpeff.SnpEff

org.snpeff.snpEffect.commandLine.SnpEffCmdGsa

All Implemented Interfaces:

CommandLine

public class SnpEffCmdGsa
extends SnpEff

Command line: Gene-Sets Analysis Perform gene set analysys

Author:

pcingola

Nested Class Summary

Nested classes/interfaces inherited from class org.snpeff.SnpEff

SnpEff.GeneDatabaseFormat, SnpEff.InputFormat, SnpEff.OutputFormat

Field Summary

Fields

Modifier and Type	Field	Description
static int	MAX_WARNS
static int	READ_INPUT_SHOW_EVERY

Fields inherited from class org.snpeff.SnpEff

args, BUILD, BUILD_DATE, canonical, canonicalFile, command, COMMAND_LINE_WIDTH, config, configFile, configOverride, customIntervalFiles, dataDir, debug, DEFAULT_COMMAND, download, expandIub, filterIntervalFiles, genomeVer, help, hgvs, hgvsForce, hgvsOld, hgvsOneLetterAa, hgvsShift, hgvsTrId, interaction, log, maxTranscriptSupportLevel, motif, multiThreaded, nextProt, nextProtKeepAllTrs, noGenome, numWorkers, onlyProtein, onlyRegulation, onlyTranscriptsFile, output, quiet, regulationTracks, REVISION, saveOutput, shiftArgs, snpEffCmd, SOFTWARE_NAME, spliceRegionExonSize, spliceRegionIntronMax, spliceRegionIntronMin, spliceSiteSize, strict, suppressOutput, treatAllAsProteinCoding, verbose, VERSION, VERSION_AUTHOR, VERSION_BUILD, VERSION_MAJOR, VERSION_SHORT

Constructor Summary

Constructors

Constructor	Description
SnpEffCmdGsa()

Method Summary

Modifier and Type	Method	Description
protected void	config()	Read config file, load & build database
void	parseArgs(java.lang.String[] args)	Parse command line arguments
boolean	run()	Run command
protected boolean	runAnalisis()	Run command
protected boolean	runAnalisisRand()	Run enrichment analysis using random scores
protected boolean	runCommands()	Read "command" lines from file.
void	usage(java.lang.String message)	Show usage and exit

Methods inherited from class org.snpeff.SnpEff

addRegulationTrack, canonical, cmd, commandLineStr, getArgs, getConfig, getConfigFile, getOutput, isOpt, load, loadConfig, loadCustomFile, loadDb, loadMarkers, main, reportValues, run, setCanonical, setConfig, setConfigFile, setDebug, setGenomeVer, setLog, setNextProt, setNextProtKeepAllTrs, setShiftHgvs, setSpliceSiteSize, setSupressOutput, setUpDownStreamLength, setVerbose, usageDb, usageGeneric, usageGenericAndDb

Methods inherited from class java.lang.Object

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

Field Detail

READ_INPUT_SHOW_EVERY

public static int READ_INPUT_SHOW_EVERY

MAX_WARNS

public static int MAX_WARNS

Constructor Detail

SnpEffCmdGsa

public SnpEffCmdGsa()

Method Detail

config

protected void config()

Read config file, load & build database

parseArgs

public void parseArgs(java.lang.String[] args)

Parse command line arguments

Specified by:

parseArgs in interface CommandLine

Overrides:

parseArgs in class SnpEff

run

public boolean run()

Run command

Specified by:

run in interface CommandLine

Overrides:

run in class SnpEff

runAnalisis

protected boolean runAnalisis()

Run command

runAnalisisRand

protected boolean runAnalisisRand()

Run enrichment analysis using random scores

runCommands

protected boolean runCommands()

Read "command" lines from file. Loads database only once to save time

Returns:

usage

public void usage(java.lang.String message)

Show usage and exit

Specified by:

usage in interface CommandLine

Overrides:

usage in class SnpEff