Package org.snpeff.snpEffect.commandLine

Class SnpEffCmdPdb

java.lang.Object

org.snpeff.SnpEff

org.snpeff.snpEffect.commandLine.SnpEffCmdPdb

All Implemented Interfaces:

CommandLine

public class SnpEffCmdPdb
extends SnpEff

PDB distance analysis

References: http://biojava.org/wiki/BioJava:CookBook:PDB:read

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 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

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

Constructor Summary

Constructors

Constructor	Description
SnpEffCmdPdb()

Method Summary

Modifier and Type	Method	Description
java.util.List<DistanceResult>	getDistanceResults()
void	initialize()	Load all data
void	loadIdMapper()
void	parseArgs(java.lang.String[] args)	Parse command line arguments
void	pdb()	PDB analysis
protected 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 file
org.biojava.nbio.structure.Structure	readPdbFile(java.lang.String pdbFileName)	Read and parse PDB file
boolean	run()	Run according to command line options
boolean	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

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_PDB_DIR

public static final java.lang.String DEFAULT_PDB_DIR

See Also:

Constant Field Values

DEFAULT_ID_MAP_FILE

public static final java.lang.String DEFAULT_ID_MAP_FILE

See Also:

Constant Field Values

DEFAULT_INTERACT_FILE

public static final java.lang.String DEFAULT_INTERACT_FILE

See Also:

Constant Field Values

PDB_EXT

public static final java.lang.String PDB_EXT

See Also:

Constant Field Values

PDB_EXT_GZ

public static final java.lang.String PDB_EXT_GZ

See Also:

Constant Field Values

PDB_EXTS

public static final java.lang.String[] PDB_EXTS

PROTEIN_INTERACTION_FILE

public static final java.lang.String PROTEIN_INTERACTION_FILE

See Also:

Constant Field Values

UNIPROT_DATABASE

public static final java.lang.String UNIPROT_DATABASE

See Also:

Constant Field Values

DEFAULT_DISTANCE_THRESHOLD

public static final double DEFAULT_DISTANCE_THRESHOLD

See Also:

Constant Field Values

DEFAULT_MAX_MISMATCH_RATE

public static final double DEFAULT_MAX_MISMATCH_RATE

See Also:

Constant Field Values

DEFAULT_PDB_MIN_AA_SEPARATION

public static final int DEFAULT_PDB_MIN_AA_SEPARATION

See Also:

Constant Field Values

DEFAULT_PDB_ORGANISM_COMMON

public static final java.lang.String DEFAULT_PDB_ORGANISM_COMMON

See Also:

Constant Field Values

DEFAULT_PDB_ORGANISM_SCIENTIFIC

public static final java.lang.String DEFAULT_PDB_ORGANISM_SCIENTIFIC

See Also:

Constant Field Values

DEFAULT_PDB_RESOLUTION

public static final double DEFAULT_PDB_RESOLUTION

See Also:

Constant Field Values

EMPTY_DISTANCES

public static final java.util.ArrayList<DistanceResult> EMPTY_DISTANCES

Constructor Detail

SnpEffCmdPdb

public SnpEffCmdPdb()

Method Detail

getDistanceResults

public java.util.List<DistanceResult> getDistanceResults()

initialize

public void initialize()

Load all data

loadIdMapper

public void loadIdMapper()

parseArgs

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

Parse command line arguments

Specified by:

parseArgs in interface CommandLine

Overrides:

parseArgs in class SnpEff

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

protected void pdbAnalysis(java.lang.String pdbFileName)

Analyze a PDB file

readPdbFile

public org.biojava.nbio.structure.Structure readPdbFile(java.lang.String pdbFileName)

Read and parse PDB file

run

public boolean run()

Description copied from class: SnpEff

Run according to command line options

Specified by:

run in interface CommandLine

Overrides:

run in class SnpEff

run

public boolean run(boolean storeResults)

setDistanceThresholdNon

public void setDistanceThresholdNon(double distanceThresholdNon)

usage

public void usage(java.lang.String message)

Show 'usage;' message and exit with an error code '-1'

Specified by:

usage in interface CommandLine

Overrides:

usage in class SnpEff

Parameters:

message -