@gmod/indexedfasta/esm/index.js

read indexed fasta and bgzipped fasta formats

import { LocalFile } from 'generic-filehandle2';
function parseSmallFasta(text) {
    return text
        .split('>')
        .filter(t => /\S/.test(t))
        .map(entryText => {
        const [defLine, ...seqLines] = entryText.split('\n');
        const [id, ...description] = defLine.split(' ');
        const sequence = seqLines.join('').replace(/\s/g, '');
        return {
            id: id,
            description: description.join(' '),
            sequence,
        };
    });
}
class FetchableSmallFasta {
    constructor({ fasta, path }) {
        if (fasta) {
            this.fasta = fasta;
        }
        else if (path) {
            this.fasta = new LocalFile(path);
        }
        else {
            throw new Error('Need to pass fasta or path');
        }
        this.data = this.fasta.readFile().then(buffer => {
            const decoder = new TextDecoder('utf8');
            const text = decoder.decode(buffer);
            return parseSmallFasta(text);
        });
    }
    async fetch(id, start, end) {
        const data = await this.data;
        const entry = data.find(iter => iter.id === id);
        const length = end - start;
        if (!entry) {
            throw new Error(`no sequence with id ${id} exists`);
        }
        return entry.sequence.slice(start, length);
    }
    async getSequenceNames() {
        const data = await this.data;
        return data.map(entry => entry.id);
    }
}
export { FetchableSmallFasta, parseSmallFasta };
export { default as BgzipIndexedFasta } from "./bgzipIndexedFasta.js";
export { default as IndexedFasta } from "./indexedFasta.js";
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