com.fulcrumgenomics.util.GeneAnnotations.scala Maven / Gradle / Ivy
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/*
* The MIT License
*
* Copyright (c) 2017 Fulcrum Genomics
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
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* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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* THE SOFTWARE.
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package com.fulcrumgenomics.util
import htsjdk.samtools.util.{CoordMath, Locatable}
import com.fulcrumgenomics.FgBioDef._
import enumeratum.EnumEntry
/** Stores classes useful for storing annotation information for genes and their transcripts and exons. */
object GeneAnnotations {
/**
* A gene with a collection of gene loci.
*/
case class Gene(name: String, loci: Seq[GeneLocus], biotype: Option[GeneBiotype] = None) extends Iterable[Transcript] {
/** Iterate over all transcripts from all GeneLoci (each a collection of transcripts). */
def iterator: Iterator[Transcript] = this.loci.iterator.flatten
/** Returns the locus with the maximum transcript mappings. */
def primaryLocus: GeneLocus = loci.maxBy(_.size)
}
/**
* A gene locus representing a set of transcripts that are mapped to the same location on the genome.
*
* @param transcripts the set of transcripts at the locus
*/
case class GeneLocus(transcripts: Seq[Transcript]) extends Locatable with Iterable[Transcript] {
require(transcripts.nonEmpty, "GeneLocus cannot be generated from an empty set of transcripts.")
require(transcripts.forall(t => t.chrom == transcripts.head.chrom))
require(transcripts.forall(t => t.negativeStrand == transcripts.head.negativeStrand))
val chrom: String = transcripts.head.chrom
val start: Int = transcripts.minBy(_.start).start
val end: Int = transcripts.maxBy(_.end).end
val negativeStrand: Boolean = transcripts.head.negativeStrand
def positiveStrand: Boolean = !negativeStrand
// Locatable implementation
override def getContig: String = chrom
override def getStart: Int = start
override def getEnd: Int = end
override def iterator: Iterator[Transcript] = this.transcripts.iterator
}
/**
* A transcript [mapping] associated with a given gene locus. Contains zero or more exons.
* The exons should be given in the order of transcription.
*/
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 {
if (exons.length > 1) {
val exonsOverlap = genomicOrder.sliding(2).map { e => (e.head, e.last) }.exists { case (e1, e2) => CoordMath.overlaps(e1.start, e1.end, e2.start, e2.end) }
require(!exonsOverlap, s"exons overlap for transcript: $name")
}
require(cdsStart.isDefined == cdsEnd.isDefined, s"cdsStart and cdsEnd must either both or neither be defined on tx: $name.")
// Locatable implementation
override def getContig: String = chrom
override def getStart: Int = start
override def getEnd: Int = end
def positiveStrand: Boolean = !negativeStrand
/** The order in which exons appear in the transcripts */
def transcriptOrder: Iterator[Exon] = exons.iterator
/** The order in which exons appear in the genome */
def genomicOrder: Iterator[Exon] = exons.sortBy { exon => (exon.start, exon.end) }.iterator
/** The length of the transcript mapping on the genome (including introns). */
def lengthOnGenome: Int = end - start + 1
/** The length of the transcribed product after introns are removed. */
def transcribedLength: Int = exons.sumBy(_.length)
/** True if the transcript is coding, false otherwise. */
def isCoding: Boolean = cdsStart.isDefined
}
/** Defines an exonic sequence within a transcript. */
case class Exon(start: Int, end: Int) {
require(start <= end, "start is greater than end when creating an exon")
def length: Int = end - start + 1
}
/** Trait that gene biotypes will extends */
sealed trait GeneBiotype extends EnumEntry {
/** The biotype name in the RefSeq GFF */
def refSeqValue: String
/** True if this biotype represents a protein coding feature */
def isCoding: Boolean
}
/** Enum to represent gene biotypes. The current list contains all values found in NCBI RefSeq GFFs circa 2021.
* In future more and/or different values from other sources may be added. */
object GeneBiotype extends FgBioEnum[GeneBiotype] {
/** All values of the GeneBiotype Enum */
def values: IndexedSeq[GeneBiotype] = findValues
/** Allows GeneBiotypes to be built from the Enum name of the biotype name from the GFF */
override def apply(str: String): GeneBiotype = values.find(_.refSeqValue == str).getOrElse(super.apply(str))
case object AntisenseRna extends GeneBiotype { val refSeqValue = "antisense_RNA"; val isCoding = false }
case object CRegion extends GeneBiotype { val refSeqValue = "C_region"; val isCoding = true }
case object DSegment extends GeneBiotype { val refSeqValue = "D_segment"; val isCoding = true }
case object GuideRna extends GeneBiotype { val refSeqValue = "guide_RNA"; val isCoding = false }
case object JSegment extends GeneBiotype { val refSeqValue = "J_segment"; val isCoding = true }
case object LncRna extends GeneBiotype { val refSeqValue = "lncRNA"; val isCoding = false }
case object MiRna extends GeneBiotype { val refSeqValue = "miRNA"; val isCoding = false }
case object MiscRna extends GeneBiotype { val refSeqValue = "misc_RNA"; val isCoding = false }
case object NcRna extends GeneBiotype { val refSeqValue = "ncRNA"; val isCoding = false }
case object Other extends GeneBiotype { val refSeqValue = "other"; val isCoding = false }
case object ProteinCoding extends GeneBiotype { val refSeqValue = "protein_coding"; val isCoding = true }
case object RNaseMrpRna extends GeneBiotype { val refSeqValue = "RNase_MRP_RNA"; val isCoding = false }
case object RNasePRna extends GeneBiotype { val refSeqValue = "RNase_P_RNA"; val isCoding = false }
case object RRna extends GeneBiotype { val refSeqValue = "rRNA"; val isCoding = false }
case object ScRna extends GeneBiotype { val refSeqValue = "scRNA"; val isCoding = false }
case object SnRna extends GeneBiotype { val refSeqValue = "snRNA"; val isCoding = false }
case object SnoRna extends GeneBiotype { val refSeqValue = "snoRNA"; val isCoding = false }
case object SrpRna extends GeneBiotype { val refSeqValue = "SRP_RNA"; val isCoding = false }
case object TRna extends GeneBiotype { val refSeqValue = "tRNA"; val isCoding = false }
case object TelomeraseRna extends GeneBiotype { val refSeqValue = "telomerase_RNA"; val isCoding = false }
case object VaultRna extends GeneBiotype { val refSeqValue = "vault_RNA"; val isCoding = false }
case object VSegment extends GeneBiotype { val refSeqValue = "V_segment"; val isCoding = false }
case object YRna extends GeneBiotype { val refSeqValue = "Y_RNA"; val isCoding = false }
}
}
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