Package org.snpeff.snpEffect.factory
Class SnpEffPredictorFactoryKnownGene
- java.lang.Object
-
- org.snpeff.snpEffect.factory.SnpEffPredictorFactory
-
- org.snpeff.snpEffect.factory.SnpEffPredictorFactoryKnownGene
-
public class SnpEffPredictorFactoryKnownGene extends SnpEffPredictorFactory
This class creates a SnpEffectPredictor from a TXT file dumped using UCSC table browser Fields in this table Field Example SQL type Info Description ----- ------- -------- ---- ----------- name uc001aaa.3 varchar(255) values Name of gene chrom chr1 varchar(255) values Reference sequence chromosome or scaffold strand + char(1) values + or - for strand txStart 11873 int(10) unsigned range Transcription start position txEnd 14409 int(10) unsigned range Transcription end position cdsStart 11873 int(10) unsigned range Coding region start cdsEnd 11873 int(10) unsigned range Coding region end exonCount 3 int(10) unsigned range Number of exons exonStarts 11873,12612,13220, longblob Exon start positions exonEnds 12227,12721,14409, longblob Exon end positions proteinID varchar(40) values UniProt display ID for Known Genes, UniProt accession or RefSeq protein ID for UCSC Genes alignID uc001aaa.3 varchar(255) values Unique identifier for each (known gene, alignment position) pair- Author:
- pcingola
-
-
Field Summary
Fields Modifier and Type Field Description static java.lang.String
CDS_STAT_COMPLETE
-
Fields inherited from class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
MARK, MIN_TOTAL_FRAME_COUNT
-
-
Constructor Summary
Constructors Constructor Description SnpEffPredictorFactoryKnownGene(Config config)
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description SnpEffectPredictor
create()
protected void
readRefSeqFile()
Read and parse genes file-
Methods inherited from class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
add, add, add, add, add, add, addMarker, addSequences, adjustChromosomes, adjustTranscripts, beforeExonSequences, codingFromCds, collapseZeroLenIntrons, createRandSequences, deleteRedundant, exonsFromCds, exonsFromCds, findGene, findGene, findMarker, findTranscript, findTranscript, getOrCreateChromosome, getProteinByTrId, parsePosition, readExonSequences, replaceTranscript, setCreateRandSequences, setDebug, setFastaFile, setFileName, setRandom, setReadSequences, setStoreSequences, setVerbose, showChromoNamesDifferences
-
-
-
-
Field Detail
-
CDS_STAT_COMPLETE
public static final java.lang.String CDS_STAT_COMPLETE
- See Also:
- Constant Field Values
-
-
Constructor Detail
-
SnpEffPredictorFactoryKnownGene
public SnpEffPredictorFactoryKnownGene(Config config)
-
-
Method Detail
-
create
public SnpEffectPredictor create()
- Specified by:
create
in classSnpEffPredictorFactory
-
readRefSeqFile
protected void readRefSeqFile()
Read and parse genes file
-
-