Package org.snpeff.snpEffect.factory
Class SnpEffPredictorFactoryGff2
java.lang.Object
org.snpeff.snpEffect.factory.SnpEffPredictorFactory
org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff2
This class creates a SnpEffectPredictor from a GFF2 file.
WARNING: GFF2 support is VERY limited! It was only done for amel (honey bee) genome.
Note: GFF2 is an obsolete format. Take a look at this quote from Gmod (http://gmod.org/wiki/GFF2)
"Why GFF2 is harmful to your health
One of GFF2's problems is that it is only able to represent one level of nesting of features. This
is mainly a problem when dealing with genes that have multiple alternatively-spliced transcripts. GFF2
is unable to deal with the three-level hierarchy of gene transcript exon. Most people get
around this by declaring a series of transcripts and giving them similar names to indicate that they
come from the same gene. The second limitation is that while GFF2 allows you to create two-level hierarchies, such
as transcript exon, it doesn't have any concept of the direction of the hierarchy. So it doesn't know
whether the exon is a subfeature of the transcript, or vice-versa. This means you have to use "aggregators" to sort
out the relationships. This is a major pain in the neck. For this reason, GFF2 format has been deprecated in
favor of GFF2 format databases."
We are only adding this format in order to read old amel2 (Honey bee) genome annotations
Refereces: http://gmod.org/wiki/GFF2
- Author:
- pcingola
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Field Summary
Fields inherited from class org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
FASTA_DELIMITER
Fields 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.SnpEffPredictorFactoryGff
addExon, addExons, addGene, addGene, addIntergenicConserved, addInterval, addIntronConserved, addUtr3, addUtr5, create, findOrCreateExon, findOrCreateGene, findOrCreateTranscript, parse, readExonSequences, readExonSequencesGff, readGff
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, replaceTranscript, setCircularCorrectLargeGap, setCreateRandSequences, setDebug, setFastaFile, setFileName, setRandom, setReadSequences, setStoreSequences, setVerbose, showChromoNamesDifferences
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Constructor Details
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SnpEffPredictorFactoryGff2
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