seqparse/dist/index.d.ts

Parse sequence files (GenBank, FASTA, SnapGene, SBOL) and accession IDs (NCBI, iGEM) to a common format

import parseFile from "./parseFile";
/** Seq is a single parsed sequence from a file or accession. */
export interface Seq {
    /** annotations of the sequence */
    annotations: Annotation[];
    /** name of the sequence */
    name: string;
    /** the sequence */
    seq: string;
    /** type of sequence. Inferred from the seq's symbols */
    type: "dna" | "rna" | "aa" | "unknown";
}
/** Annotation is a single feature/annotation parsed from a sequence file. */
export interface Annotation {
    /** color of the annotation if set */
    color?: string;
    /** 1 if forward, 0 if no direction, -1 if in reverse direction */
    direction?: number;
    /** end of the annotation, 0-based */
    end: number;
    /** name of the annotation */
    name: string;
    /** start of the annotation, 0-based */
    start: number;
    /** type field if set on the annotation */
    type?: string;
}
/** Options to parse sequence files. */
export interface ParseOptions {
    /**
     * Whether to use cors-anywhere to circumvent iGEM's web server having a bad configuration.
     */
    cors?: boolean;
    /** name of the source file */
    fileName?: string;
    /**
     * Source of the file (ArrayBuffer). This is necessary for SnapGene.
     *
     * Eg after a read from FileReader.readAsArrayBuffer() in a browser:
     * https://developer.mozilla.org/en-US/docs/Web/API/FileReader/readAsArrayBuffer
     */
    source?: ArrayBuffer;
}
declare const _default: (input: string, options?: ParseOptions) => Promise<Seq>;
export default _default;
export { parseFile };