BioKotlin/biokotlin.seq/ProteinSeqRecord

ProteinSeqRecord

class ProteinSeqRecord(val sequence: ProteinSeq, val id: String, val name: String? = null, val description: String? = null, val annotations: ImmutableMap<String, String> = ImmutableMap.of(), val letterAnnotations: ImmutableMap<String, Array<out Any>> = ImmutableMap.of()) : SeqRecord, ProteinSeq

A ProteinSeqRecord consists of a ProteinSeq and several optional annotations.

Main attributes:

id - Identifier such as a locus tag (string)
seq - The sequence itself (ProteinSeq) Additional attributes:
name - Sequence name, e.g. gene name (string)
description - Additional text (string)
annotations - A map of strings containing key-value pairs of annotations for different features
letterAnnotations - Per letter/symbol annotation. This holds an ImmutableList whose length matches that of the sequence. A typical use would be to hold a list of integers representing sequencing quality scores.

from Bio.Seq import ProteinSeq from Bio.Seq import ProteinSeqRecord val record_1 = ProteinSeqRecord(ProteinSeq("UX"), "1", "seq1", "the first sequence")

Constructors

ProteinSeqRecord

constructor(sequence: ProteinSeq, id: String, name: String? = null, description: String? = null, annotations: ImmutableMap<String, String> = ImmutableMap.of(), letterAnnotations: ImmutableMap<String, Array<out Any>> = ImmutableMap.of())

Properties

annotations

val annotations: ImmutableMap<String, String>

description

val description: String?

val id: String

letterAnnotations

val letterAnnotations: ImmutableMap<String, Array<out Any>>

name

val name: String?

sequence

val sequence: ProteinSeq

Functions

back_translate

open override fun back_translate(): NucSeq

compareTo

open operator override fun compareTo(other: Seq): Int

contains

open operator override fun contains(element: ProteinSeq): Boolean

copyOfBytes

open override fun copyOfBytes(): ByteArray

count

open override fun count(query: AminoAcid): Int

open override fun count(query: ProteinSeq): Int

count_overlap

open override fun count_overlap(query: ProteinSeq): Int

find

open override fun find(query: ProteinSeq, start: Int, end: Int): Int

get

open operator override fun get(i: Int): AminoAcid

Returns on AminoAcid at the given position, if negative returns from the end of the sequence

open operator override fun get(x: IntRange): ProteinSeq

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 residues)