Package org.snpeff.snpEffect.commandLine
Class SnpEffCmdPdb
java.lang.Object
org.snpeff.SnpEff
org.snpeff.snpEffect.commandLine.SnpEffCmdPdb
- All Implemented Interfaces:
CommandLine
PDB distance analysis
References: http://biojava.org/wiki/BioJava:CookBook:PDB:read
- 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
FieldsModifier and TypeFieldDescriptionstatic final double
static final String
static final String
static final double
static final String
static final int
static final String
static final String
static final double
static final ArrayList<DistanceResult>
static final String
static final String
static final String[]
static final String
static final String
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 -
Method Summary
Modifier and TypeMethodDescriptionvoid
Load all datavoid
void
Parse command line argumentsvoid
pdb()
PDB analysisprotected void
Check that protein sequences form PDB matches sequences from Genome Return an IdMapped of confirmed entries (i.e.protected void
pdbAnalysis
(String pdbFileName) Analyze a PDB fileorg.biojava.nbio.structure.Structure
readPdbFile
(String pdbFileName) Read and parse PDB fileboolean
run()
Run according to command line optionsboolean
run
(boolean storeResults) void
setDistanceThresholdNon
(double distanceThresholdNon) void
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 Details
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DEFAULT_PDB_DIR
- See Also:
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DEFAULT_ID_MAP_FILE
- See Also:
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DEFAULT_INTERACT_FILE
- See Also:
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PDB_EXT
- See Also:
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PDB_EXT_GZ
- See Also:
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PDB_EXTS
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PROTEIN_INTERACTION_FILE
- See Also:
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UNIPROT_DATABASE
- See Also:
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DEFAULT_DISTANCE_THRESHOLD
public static final double DEFAULT_DISTANCE_THRESHOLD- See Also:
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DEFAULT_MAX_MISMATCH_RATE
public static final double DEFAULT_MAX_MISMATCH_RATE- See Also:
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DEFAULT_PDB_MIN_AA_SEPARATION
public static final int DEFAULT_PDB_MIN_AA_SEPARATION- See Also:
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DEFAULT_PDB_ORGANISM_COMMON
- See Also:
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DEFAULT_PDB_ORGANISM_SCIENTIFIC
- See Also:
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DEFAULT_PDB_RESOLUTION
public static final double DEFAULT_PDB_RESOLUTION- See Also:
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EMPTY_DISTANCES
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Constructor Details
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SnpEffCmdPdb
public SnpEffCmdPdb()
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Method Details
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getDistanceResults
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initialize
public void initialize()Load all data -
loadIdMapper
public void loadIdMapper() -
parseArgs
Parse command line arguments- Specified by:
parseArgs
in interfaceCommandLine
- Overrides:
parseArgs
in classSnpEff
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pdb
public void pdb()PDB analysis -
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) -
pdbAnalysis
Analyze a PDB file -
readPdbFile
Read and parse PDB file -
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) -
setDistanceThresholdNon
public void setDistanceThresholdNon(double distanceThresholdNon) -
usage
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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