Package org.snpeff.snpEffect.commandLine
Class SnpEffCmdProtein
- java.lang.Object
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- org.snpeff.SnpEff
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- org.snpeff.snpEffect.commandLine.SnpEffCmdProtein
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- All Implemented Interfaces:
CommandLine
public class SnpEffCmdProtein extends SnpEff
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
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Nested classes/interfaces inherited from class org.snpeff.SnpEff
SnpEff.GeneDatabaseFormat, SnpEff.InputFormat, SnpEff.OutputFormat
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Field Summary
Fields Modifier and Type Field Description static double
MAX_ERROR_RATE
static boolean
onlyOneError
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Fields 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
Constructors Constructor Description SnpEffCmdProtein()
SnpEffCmdProtein(java.lang.String genomeVer, java.lang.String configFile, java.lang.String proteinFile)
SnpEffCmdProtein(Config config)
SnpEffCmdProtein(Config config, java.lang.String proteinFile)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description static int
diffCount(java.lang.String s1, java.lang.String s2)
Count number of differences between stringsstatic java.lang.String
diffStr(java.lang.String s1, java.lang.String s2)
Show difference between two stringsjava.util.HashMap<java.lang.String,SmithWaterman>
getAlignmentByTrId()
int
getTotalErrors()
int
getTotalOk()
void
parseArgs(java.lang.String[] args)
Parse command line argumentsboolean
run()
Run commandvoid
setCheckNumOk(boolean checkNumOk)
void
setProteinByTrId(java.util.Map<java.lang.String,java.lang.String> proteinByTrId)
void
setStoreAlignments(boolean storeAlignments)
void
usage(java.lang.String message)
Show usage and exit-
Methods inherited from class org.snpeff.SnpEff
addRegulationTrack, canonical, cmd, commandLineStr, error, fatalError, 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, warning
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Constructor Detail
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SnpEffCmdProtein
public SnpEffCmdProtein()
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SnpEffCmdProtein
public SnpEffCmdProtein(Config config)
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SnpEffCmdProtein
public SnpEffCmdProtein(Config config, java.lang.String proteinFile)
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SnpEffCmdProtein
public SnpEffCmdProtein(java.lang.String genomeVer, java.lang.String configFile, java.lang.String proteinFile)
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Method Detail
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diffCount
public static int diffCount(java.lang.String s1, java.lang.String s2)
Count number of differences between strings
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diffStr
public static java.lang.String diffStr(java.lang.String s1, java.lang.String s2)
Show difference between two strings
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getAlignmentByTrId
public java.util.HashMap<java.lang.String,SmithWaterman> getAlignmentByTrId()
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getTotalErrors
public int getTotalErrors()
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getTotalOk
public int getTotalOk()
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parseArgs
public void parseArgs(java.lang.String[] args)
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)
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setProteinByTrId
public void setProteinByTrId(java.util.Map<java.lang.String,java.lang.String> proteinByTrId)
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setStoreAlignments
public void setStoreAlignments(boolean storeAlignments)
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usage
public void usage(java.lang.String message)
Show usage and exit- Specified by:
usage
in interfaceCommandLine
- Overrides:
usage
in classSnpEff
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