readFASTA static method

Future<List<Map<String, String>>> readFASTA({ String? path, String? str, })

Returns sequences from either a file path or str in FASTA format.

Each map contains a sequence seq, ID id, and description desc.

Implementation

static Future<List<Map<String, String>>> readFASTA({String? path, String? str}) async {
  String? contents;
  if (path != null) {
    contents = await File(path).readAsString();
  } else if (str != null) {
    contents = str;
  } else {
    Errors.invalidFASTAArgs();
  }

  List<String> lines = contents!.split('\n');
  int seqCount = 0;

  List<Map<String, String>> fastaMaps = [];
  Map<String, String> currentMap = {};

  for (var line in lines) {
    if (line.startsWith('>')) {
      if (seqCount != 0) {
        fastaMaps.add(currentMap);
        currentMap = {};
      }
      seqCount++;
      currentMap[kSeq] = '';

      String topLine = line.split('>')[1];
      List<String> topLineList = topLine.split(' ');

      currentMap[kId] = topLineList.first;
      currentMap[kDesc] = topLineList.sublist(1, topLineList.length).join(" ");
    } else {
      currentMap[kSeq] = currentMap[kSeq]! + line;
    }
  }
  fastaMaps.add(currentMap);
  return fastaMaps;
}