@jbrowse/plugin-config/dist/NcbiSequenceReportAliasAdapter/NcbiSequenceReportAliasAdapter.js

JBrowse 2 config utilities

"use strict";
Object.defineProperty(exports, "__esModule", { value: true });
const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
const io_1 = require("@jbrowse/core/util/io");
class NcbiSequenceReportAliasAdapter extends BaseAdapter_1.BaseAdapter {
    async getRefNameAliases() {
        const loc = this.getConf('location');
        if (loc.uri === '' || loc.uri === '/path/to/my/sequence_report.tsv') {
            return [];
        }
        const override = this.getConf('useNameOverride');
        const results = await (0, io_1.openLocation)(loc, this.pluginManager).readFile('utf8');
        const lines = results
            .split(/\n|\r\n|\r/)
            .filter(f => !!f.trim())
            .map(row => row.split('\t'));
        const r = lines[0] || [];
        const genBankIdx = r.indexOf('GenBank seq accession');
        const refSeqIdx = r.indexOf('RefSeq seq accession');
        const ucscIdx = r.indexOf('UCSC style name');
        const seqNameIdx = r.indexOf('Sequence name');
        if (genBankIdx === -1 || refSeqIdx === -1 || ucscIdx === -1) {
            throw new Error('Header line must include "GenBank seq accession", "RefSeq seq accession", "UCSC style name", and "Sequence name"');
        }
        return lines
            .slice(1)
            .filter(cols => !!cols[ucscIdx] || !!cols[seqNameIdx])
            .map(cols => ({
            refName: (cols[ucscIdx] || cols[seqNameIdx]),
            aliases: [
                cols[genBankIdx],
                cols[refSeqIdx],
                cols[ucscIdx],
                cols[seqNameIdx],
            ].filter((f) => !!f),
            override,
        }))
            .filter(f => !!f.refName);
    }
}
exports.default = NcbiSequenceReportAliasAdapter;