BioKotlin/biokotlin.seq/NucSeq

NucSeq

interface NucSeq : Seq

Main data structure for working with DNA and RNA sequences

Inheritors

Properties

abstract val nucSet: NucSet

The type of nucleotides - DNA or RNA and ambiguous or not

Functions

back_transcribe

abstract fun back_transcribe(): NucSeq

Transcribes a NucSeq - essentially changes the NucSet from NUC.RNA to NUC.DNA

abstract operator fun compareTo(other: Seq): Int

abstract fun complement(): NucSeq

Returns the complement sequence of DNA or RNA, ambiguity is preserved

abstract operator fun contains(element: NucSeq): Boolean

abstract fun copyOfBytes(): ByteArray

abstract fun count(query: NUC): Int

abstract fun count(query: NucSeq): Int

abstract fun count_overlap(query: NucSeq): Int

open fun find(query: NucSeq, start: Int = 0, end: Int = Int.MAX_VALUE): Int

abstract fun gc(): Int

Counts the NUC.G + NUC.C within a NucSeq

abstract operator fun get(i: Int): NUC

Returns the NUC of this NucSeq at the specified index i with i starting at zero Negative index start from the end of the sequence, i.e. -1 is the last base

abstract operator fun get(x: IntRange): NucSeq

Returns a subset NucSeq based on the IntRange of Nucleotides. Kotlin range operator is "..". Indices start at zero. Note Kotlin IntRange are inclusive end, while Python slices exclusive end Negative slices "-3..-1" start from the last base (i.e. would return the last three bases)

abstract operator fun get(i: Int, j: Int): NucSeq

Returns a subset NucSeq based on the inclusive start i and inclusive last j Indices start at zero. Negative index start from the end of the sequence, i.e. -1 is the last base

abstract fun indexOf(query: NucSeq, start: Int = 0, end: Int = Int.MAX_VALUE): Int

abstract fun join(vararg seqs: NucSeq): NucSeq

open fun kmers(kmerSize: Int = 21, bothStrands: Boolean = true, stepSize: Int = 1): KmerMultiSet

Extracts the kmer count from a nucleotide sequence NucSeq. In general kmers from both strands should be extracted, unless strand specificity is really known. No kmers that include an ambiguous base pair will be included Using stepSize subsets of the kmers can be sampled

abstract fun lastIndexOf(query: NucSeq, start: Int = Int.MAX_VALUE, end: Int = 0): Int

abstract operator fun plus(seq2: NucSeq): NucSeq

abstract fun repr(): String

Returns (truncated) representation of the sequence for debugging

reverse_complement

abstract fun reverse_complement(): NucSeq

Returns the complement sequence of DNA or RNA

open fun rfind(query: NucSeq, start: Int = Int.MAX_VALUE, end: Int = 0): Int

abstract fun seq(): String

abstract fun size(): Int

Returns the length of the sequence

abstract operator fun times(n: Int): NucSeq

abstract override fun toString(): String

Return the full sequence as string

abstract fun transcribe(): NucSeq

Transcribes a NucSeq - essentially changes the NucSet from NUC.DNA to NUC.RNA

abstract fun translate(table: CodonTable = CodonTable(1), to_stop: Boolean = false, cds: Boolean = false): ProteinSeq

Translate a nucleotide sequence NucSeq into amino acids ProteinSeq.

abstract fun ungap(): Seq

TODO - needs to be implemented