Package org.snpsift
Class SnpSiftCmdDbNsfp
- java.lang.Object
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- org.snpsift.SnpSift
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- org.snpsift.SnpSiftCmdDbNsfp
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- All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine
,org.snpeff.snpEffect.VcfAnnotator
public class SnpSiftCmdDbNsfp extends SnpSift
Annotate a VCF file with dbNSFP.The dbNSFP is an integrated database of functional predictions from multiple algorithms for the comprehensive collection of human non-synonymous SNPs (NSs). Its current version (ver 1.1) is based on CCDS version 20090327 and includes a total of 75,931,005 NSs. It compiles prediction scores from four prediction algorithms (SIFT, Polyphen2, LRT and MutationTaster), two conservation scores (PhyloP and GERP++) and other related information.
References:
http://sites.google.com/site/jpopgen/dbNSFP
Paper: Liu X, Jian X, and Boerwinkle E. 2011. dbNSFP: a lightweight database of human non-synonymous SNPs and their functional predictions. Human Mutation. 32:894-899.
- Author:
- lletourn
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Field Summary
Fields Modifier and Type Field Description protected boolean
annotateEmpty
protected boolean
annotateMissing
protected boolean
collapseRepeatedValues
java.lang.String
CONFIG_DBNSFP_DB_NAME
protected int
count
protected int
countAnnotated
protected int
countVariants
protected DbNsfpEntry
currentDbEntry
protected DbNsfp
dbNsfp
static java.lang.String
DBNSFP_VCF_INFO_PREFIX
static java.lang.String
DEFAULT_FIELDS_NAMES_TO_ADD
protected java.util.Map<java.lang.String,java.lang.String>
fieldsDescription
protected java.lang.String
fieldsNamesToAdd
protected java.util.Map<java.lang.String,java.lang.String>
fieldsToAdd
protected java.util.Map<java.lang.String,java.lang.String>
fieldsType
protected boolean
inverseFieldSelection
static int
MIN_JUMP
static int
SHOW_EVERY
protected boolean
tabixCheck
protected org.snpeff.fileIterator.VcfFileIterator
vcfFile
protected java.lang.String
vcfFileName
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Fields inherited from class org.snpsift.SnpSift
args, BUILD, command, config, configFile, dataDir, dbFileName, dbTabix, dbType, debug, download, EMPTY_ARGS, errCount, genomeVersion, help, log, needsConfig, needsDb, needsGenome, numWorkers, output, quiet, REVISION, saveOutput, shiftArgs, SHOW_EVERY_VCFLINES, showVcfHeader, showVersion, SOFTWARE_NAME, suppressOutput, vcfHeaderAddProgramVersion, vcfHeaderProcessed, vcfInputFile, verbose, VERSION, VERSION_MAJOR, VERSION_NO_NAME, VERSION_SHORT
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Constructor Summary
Constructors Constructor Description SnpSiftCmdDbNsfp()
SnpSiftCmdDbNsfp(java.lang.String[] args)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
addHeaders(org.snpeff.fileIterator.VcfFileIterator vcfFile)
Add some lines to header before showing itboolean
annotate(org.snpeff.interval.Variant variant, java.util.Map<java.lang.String,java.lang.String> info)
Annotate a VCF entryboolean
annotate(org.snpeff.vcf.VcfEntry vcfEntry)
boolean
annotateFinish(org.snpeff.fileIterator.VcfFileIterator vcfFile)
boolean
annotateInit(org.snpeff.fileIterator.VcfFileIterator vcfFile)
Initialize annotation processvoid
checkFieldsToAdd()
Check that all fields to add are availablejava.util.Map<java.lang.String,java.lang.String>
getFieldsType()
void
init()
Initialize default valuesvoid
parseArgs(java.lang.String[] args)
Parse command line argumentsboolean
run()
java.util.List<org.snpeff.vcf.VcfEntry>
run(boolean createList)
Run annotation algorithmvoid
setFieldsNamesToAdd(java.lang.String fieldsNamesToAdd)
void
setTabixCheck(boolean tabixCheck)
void
usage(java.lang.String msg)
Show usage message-
Methods inherited from class org.snpsift.SnpSift
cmd, commandLineStr, databaseDownload, databaseFind, error, getArgs, getConfig, getConfigFile, getOutput, headers, isOpt, loadConfig, main, openVcfInputFile, processVcfHeader, setCommand, setCommand, setConfig, setConfigFile, setDbFileName, setDebug, setQuiet, setSaveOutput, setShowVcfHeader, setShowVersion, setSuppressOutput, setVcfHeaderAddProgramVersion, setVerbose, showCmd, showVersion, unSanitize, usageGenericAndDb
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Field Detail
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DBNSFP_VCF_INFO_PREFIX
public static final java.lang.String DBNSFP_VCF_INFO_PREFIX
- See Also:
- Constant Field Values
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DEFAULT_FIELDS_NAMES_TO_ADD
public static final java.lang.String DEFAULT_FIELDS_NAMES_TO_ADD
- See Also:
- Constant Field Values
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MIN_JUMP
public static final int MIN_JUMP
- See Also:
- Constant Field Values
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SHOW_EVERY
public static final int SHOW_EVERY
- See Also:
- Constant Field Values
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CONFIG_DBNSFP_DB_NAME
public final java.lang.String CONFIG_DBNSFP_DB_NAME
- See Also:
- Constant Field Values
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fieldsToAdd
protected java.util.Map<java.lang.String,java.lang.String> fieldsToAdd
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fieldsDescription
protected java.util.Map<java.lang.String,java.lang.String> fieldsDescription
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fieldsType
protected java.util.Map<java.lang.String,java.lang.String> fieldsType
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annotateEmpty
protected boolean annotateEmpty
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annotateMissing
protected boolean annotateMissing
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collapseRepeatedValues
protected boolean collapseRepeatedValues
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inverseFieldSelection
protected boolean inverseFieldSelection
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tabixCheck
protected boolean tabixCheck
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vcfFileName
protected java.lang.String vcfFileName
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count
protected int count
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countAnnotated
protected int countAnnotated
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countVariants
protected int countVariants
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dbNsfp
protected DbNsfp dbNsfp
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vcfFile
protected org.snpeff.fileIterator.VcfFileIterator vcfFile
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currentDbEntry
protected DbNsfpEntry currentDbEntry
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fieldsNamesToAdd
protected java.lang.String fieldsNamesToAdd
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Method Detail
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addHeaders
public boolean addHeaders(org.snpeff.fileIterator.VcfFileIterator vcfFile)
Add some lines to header before showing it- Specified by:
addHeaders
in interfaceorg.snpeff.snpEffect.VcfAnnotator
- Overrides:
addHeaders
in classSnpSift
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annotate
public boolean annotate(org.snpeff.interval.Variant variant, java.util.Map<java.lang.String,java.lang.String> info)
Annotate a VCF entry- Parameters:
info
- Add values to 'info' map. Note that we may have some previous values in the map- Returns:
- True if entries were added to the map
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annotate
public boolean annotate(org.snpeff.vcf.VcfEntry vcfEntry)
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annotateFinish
public boolean annotateFinish(org.snpeff.fileIterator.VcfFileIterator vcfFile)
- Specified by:
annotateFinish
in interfaceorg.snpeff.snpEffect.VcfAnnotator
- Overrides:
annotateFinish
in classSnpSift
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annotateInit
public boolean annotateInit(org.snpeff.fileIterator.VcfFileIterator vcfFile)
Initialize annotation process- Specified by:
annotateInit
in interfaceorg.snpeff.snpEffect.VcfAnnotator
- Overrides:
annotateInit
in classSnpSift
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checkFieldsToAdd
public void checkFieldsToAdd() throws java.io.IOException
Check that all fields to add are available- Throws:
java.io.IOException
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getFieldsType
public java.util.Map<java.lang.String,java.lang.String> getFieldsType()
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parseArgs
public void parseArgs(java.lang.String[] args)
Parse command line arguments
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run
public boolean run()
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run
public java.util.List<org.snpeff.vcf.VcfEntry> run(boolean createList)
Run annotation algorithm
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setFieldsNamesToAdd
public void setFieldsNamesToAdd(java.lang.String fieldsNamesToAdd)
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setTabixCheck
public void setTabixCheck(boolean tabixCheck)
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