Package org.snpeff.snpEffect.commandLine
Class SnpEffCmdPdb
- java.lang.Object
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- org.snpeff.SnpEff
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- org.snpeff.snpEffect.commandLine.SnpEffCmdPdb
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- All Implemented Interfaces:
CommandLine
public class SnpEffCmdPdb extends SnpEff
PDB distance analysisReferences: http://biojava.org/wiki/BioJava:CookBook:PDB:read
- 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
DEFAULT_DISTANCE_THRESHOLD
static java.lang.String
DEFAULT_ID_MAP_FILE
static java.lang.String
DEFAULT_INTERACT_FILE
static double
DEFAULT_MAX_MISMATCH_RATE
static java.lang.String
DEFAULT_PDB_DIR
static int
DEFAULT_PDB_MIN_AA_SEPARATION
static java.lang.String
DEFAULT_PDB_ORGANISM_COMMON
static java.lang.String
DEFAULT_PDB_ORGANISM_SCIENTIFIC
static double
DEFAULT_PDB_RESOLUTION
static java.util.ArrayList<DistanceResult>
EMPTY_DISTANCES
static java.lang.String
PDB_EXT
static java.lang.String
PDB_EXT_GZ
static java.lang.String[]
PDB_EXTS
static java.lang.String
PROTEIN_INTERACTION_FILE
static java.lang.String
UNIPROT_DATABASE
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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, 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 SnpEffCmdPdb()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description java.util.List<DistanceResult>
getDistanceResults()
void
initialize()
Load all datavoid
loadIdMapper()
void
parseArgs(java.lang.String[] args)
Parse command line argumentsvoid
pdb()
PDB analysisprotected void
pdbAnalysis()
Check that protein sequences form PDB matches sequences from Genome Return an IdMapped of confirmed entries (i.e.protected void
pdbAnalysis(java.lang.String pdbFileName)
Analyze a PDB fileorg.biojava.nbio.structure.Structure
readPdbFile(java.lang.String pdbFileName)
Read and parse PDB fileboolean
run()
Run according to command line optionsboolean
run(boolean storeResults)
void
setDistanceThresholdNon(double distanceThresholdNon)
void
usage(java.lang.String message)
Show 'usage;' message and exit with an error code '-1'-
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
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Field Detail
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DEFAULT_PDB_DIR
public static final java.lang.String DEFAULT_PDB_DIR
- See Also:
- Constant Field Values
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DEFAULT_ID_MAP_FILE
public static final java.lang.String DEFAULT_ID_MAP_FILE
- See Also:
- Constant Field Values
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DEFAULT_INTERACT_FILE
public static final java.lang.String DEFAULT_INTERACT_FILE
- See Also:
- Constant Field Values
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PDB_EXT
public static final java.lang.String PDB_EXT
- See Also:
- Constant Field Values
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PDB_EXT_GZ
public static final java.lang.String PDB_EXT_GZ
- See Also:
- Constant Field Values
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PDB_EXTS
public static final java.lang.String[] PDB_EXTS
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PROTEIN_INTERACTION_FILE
public static final java.lang.String PROTEIN_INTERACTION_FILE
- See Also:
- Constant Field Values
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UNIPROT_DATABASE
public static final java.lang.String UNIPROT_DATABASE
- See Also:
- Constant Field Values
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DEFAULT_DISTANCE_THRESHOLD
public static final double DEFAULT_DISTANCE_THRESHOLD
- See Also:
- Constant Field Values
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DEFAULT_MAX_MISMATCH_RATE
public static final double DEFAULT_MAX_MISMATCH_RATE
- See Also:
- Constant Field Values
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DEFAULT_PDB_MIN_AA_SEPARATION
public static final int DEFAULT_PDB_MIN_AA_SEPARATION
- See Also:
- Constant Field Values
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DEFAULT_PDB_ORGANISM_COMMON
public static final java.lang.String DEFAULT_PDB_ORGANISM_COMMON
- See Also:
- Constant Field Values
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DEFAULT_PDB_ORGANISM_SCIENTIFIC
public static final java.lang.String DEFAULT_PDB_ORGANISM_SCIENTIFIC
- See Also:
- Constant Field Values
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DEFAULT_PDB_RESOLUTION
public static final double DEFAULT_PDB_RESOLUTION
- See Also:
- Constant Field Values
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EMPTY_DISTANCES
public static final java.util.ArrayList<DistanceResult> EMPTY_DISTANCES
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Method Detail
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getDistanceResults
public java.util.List<DistanceResult> getDistanceResults()
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initialize
public void initialize()
Load all data
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loadIdMapper
public void loadIdMapper()
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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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pdb
public void pdb()
PDB analysis
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pdbAnalysis
protected void pdbAnalysis()
Check that protein sequences form PDB matches sequences from Genome Return an IdMapped of confirmed entries (i.e. AA sequence matches between transcript and PDB)
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pdbAnalysis
protected void pdbAnalysis(java.lang.String pdbFileName)
Analyze a PDB file
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readPdbFile
public org.biojava.nbio.structure.Structure readPdbFile(java.lang.String pdbFileName)
Read and parse PDB file
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run
public boolean run()
Description copied from class:SnpEff
Run according to command line options- Specified by:
run
in interfaceCommandLine
- Overrides:
run
in classSnpEff
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run
public boolean run(boolean storeResults)
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setDistanceThresholdNon
public void setDistanceThresholdNon(double distanceThresholdNon)
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usage
public void usage(java.lang.String message)
Show 'usage;' message and exit with an error code '-1'- Specified by:
usage
in interfaceCommandLine
- Overrides:
usage
in classSnpEff
- Parameters:
message
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