Package org.snpeff.snpEffect.commandLine
Class SnpEffCmdProtein
java.lang.Object
org.snpeff.SnpEff
org.snpeff.snpEffect.commandLine.SnpEffCmdProtein
- All Implemented Interfaces:
CommandLine
Command line: Read protein sequences from a file and compare them to the ones calculated from our data structures
Note: This is done in order to see potential incompatibility
errors between genome sequence and annotation.
- Author:
- pcingola
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Nested Class Summary
Nested classes/interfaces inherited from class org.snpeff.SnpEff
SnpEff.GeneDatabaseFormat, SnpEff.InputFormat, SnpEff.OutputFormat
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Field Summary
FieldsFields inherited from class org.snpeff.SnpEff
args, BUILD, BUILD_DATE, canonical, canonicalFile, command, COMMAND_LINE_WIDTH, config, configOverride, customIntervalFiles, dataDir, debug, DEFAULT_COMMAND, download, expandIub, filterIntervalFiles, genome, 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, upDownStreamLength, verbose, VERSION, VERSION_AUTHOR, VERSION_BUILD, VERSION_MAJOR, VERSION_SHORT
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Constructor Summary
ConstructorsConstructorDescriptionSnpEffCmdProtein
(String genomeVer, String configFile, String proteinFile) SnpEffCmdProtein
(Config config) SnpEffCmdProtein
(Config config, String proteinFile) -
Method Summary
Modifier and TypeMethodDescriptionstatic int
Count number of differences between stringsstatic String
Show difference between two stringsint
int
int
int
void
Parse command line argumentsboolean
run()
Run commandvoid
setCheckNumOk
(boolean checkNumOk) void
setMaxErrorRate
(double maxErrorRate) void
setProteinByTrId
(Map<String, String> proteinByTrId) void
setStoreAlignments
(boolean storeAlignments) void
Show usage and exitMethods 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
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Field Details
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onlyOneError
public static boolean onlyOneError -
MAX_ERROR_RATE
public static double MAX_ERROR_RATE
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Constructor Details
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SnpEffCmdProtein
public SnpEffCmdProtein() -
SnpEffCmdProtein
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SnpEffCmdProtein
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SnpEffCmdProtein
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Method Details
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diffCount
Count number of differences between strings -
diffStr
Show difference between two strings -
getAlignmentByTrId
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getTotalErrors
public int getTotalErrors() -
getTotalNotFound
public int getTotalNotFound() -
getTotalOk
public int getTotalOk() -
getTotalWarnings
public int getTotalWarnings() -
parseArgs
Parse command line arguments- Specified by:
parseArgs
in interfaceCommandLine
- Overrides:
parseArgs
in classSnpEff
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run
public boolean run()Run command- Specified by:
run
in interfaceCommandLine
- Overrides:
run
in classSnpEff
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setCheckNumOk
public void setCheckNumOk(boolean checkNumOk) -
setProteinByTrId
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setMaxErrorRate
public void setMaxErrorRate(double maxErrorRate) -
setStoreAlignments
public void setStoreAlignments(boolean storeAlignments) -
usage
Show usage and exit- Specified by:
usage
in interfaceCommandLine
- Overrides:
usage
in classSnpEff
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