Parsing GenBank files with multiline qualifiers ignores newlines

[nicolazilio]

Hello,

I would like to report an issue related to parsing GenBank files that contain multiline qualifiers, for example, see plannot_description

rep_origin      12..467
                    /label="f1 ori"
                    /plannot_database="snapgene"
                    /plannot_description="f1 bacteriophage origin of
                    replication; arrow indicates direction of (+) strand
                    synthesis "
                    /plannot_sseqid="f1_ori_(3)"

in the resulting json file produced by anyToJson, this is the output

{
  "notes": {
    "plannot_database": [
      "snapgene"
    ],
    "plannot_description": [
      "f1 bacteriophage origin ofreplication; arrow indicates direction of (+) strandsynthesis "
    ],
    "plannot_sseqid": [
      "f1_ori_(3)"
    ]
  },
  "type": "rep_origin",
  "strand": 1,
  "forward": true,
  "name": "f1 ori",
  "start": 11,
  "end": 466
}

As you can see, newline characters in the original GenBank qualifier are ignored and lines are simply merged together.

I would expect the parser to either preserve a newline character or, probably better, use a whitespace character.

This is the snippet of code that I use for the conversion

import fs from "fs/promises";
import path from "path";
import { anyToJson, snapgeneToJson } from "@teselagen/bio-parsers";

const SUPPORTED_GENBANK = new Set([".gbk", ".gb"]);
const SUPPORTED_SNAPGENE = new Set([".dna"]);

async function parseMapFile(filePath) {
  const ext = path.extname(filePath).toLowerCase();
  const raw = await fs.readFile(filePath);

  const input =
    SUPPORTED_GENBANK.has(ext)
      ? raw.toString("utf8")
      : SUPPORTED_SNAPGENE.has(ext)
        ? new Blob([raw], { type: "application/octet-stream" })
        : raw;

  return anyToJson(input, { fileName: path.basename(filePath) });
}

async function main() {
  const filePath = process.argv[2];
  if (!filePath) {
    console.error("Usage: node parseMapFile.mjs <map-file>");
    process.exit(1);
  }

  const parsed = await parseMapFile(filePath);
  console.log(JSON.stringify(parsed, null, 2));
}

main().catch((err) => {
  console.error("Failed to parse file:", err);
  process.exit(1);
});

Example input and output are attached.

Thank you in advance.

{
  "dependencies": {
    "@teselagen/bio-parsers": "^0.4.38"
  }
}

test_plasmid.zip