Package org.snpeff.snpEffect.factory
Class SnpEffPredictorFactoryKnownGene
java.lang.Object
org.snpeff.snpEffect.factory.SnpEffPredictorFactory
org.snpeff.snpEffect.factory.SnpEffPredictorFactoryKnownGene
This class creates a SnpEffectPredictor from a TXT file dumped using UCSC table browser
Fields in this table
Field Example SQL type Info Description
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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
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Field Summary
FieldsFields inherited from class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
MARK, MIN_TOTAL_FRAME_COUNT
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Constructor Summary
Constructors -
Method Summary
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, setCircularCorrectLargeGap, setCreateRandSequences, setDebug, setFastaFile, setFileName, setRandom, setReadSequences, setStoreSequences, setVerbose, showChromoNamesDifferences
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Field Details
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CDS_STAT_COMPLETE
- See Also:
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Constructor Details
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SnpEffPredictorFactoryKnownGene
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Method Details
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create
- Specified by:
create
in classSnpEffPredictorFactory
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readRefSeqFile
protected void readRefSeqFile()Read and parse genes file
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