object GeneAnnotations
Stores classes useful for storing annotation information for genes and their transcripts and exons.
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case class
Exon(start: Int, end: Int) extends Product with Serializable
Defines an exonic sequence within a transcript.
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case class
Gene(name: String, loci: Seq[GeneLocus]) extends Iterable[Transcript] with Product with Serializable
A gene with a collection of gene loci.
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case class
GeneLocus(transcripts: Seq[Transcript]) extends Locatable with Iterable[Transcript] with Product with Serializable
A gene locus representing a set of transcripts that are mapped to the same location on the genome.
A gene locus representing a set of transcripts that are mapped to the same location on the genome.
- transcripts
the set of transcripts at the locus
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case class
Transcript(name: String, chrom: String, start: Int, end: Int, cdsStart: Option[Int] = None, cdsEnd: Option[Int] = None, negativeStrand: Boolean, exons: Seq[Exon]) extends Locatable with Product with Serializable
A transcript [mapping] associated with a given gene locus.
A transcript [mapping] associated with a given gene locus. Contains zero or more exons. The exons should be given in the order of transcription.
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