@jbrowse/plugin-gff3 1.6.8 → 1.7.1

package/dist/Gff3Adapter/Gff3Adapter.d.ts

@@ -1,17 +1,17 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { NoAssemblyRegion } from '@jbrowse/core/util/types';
-import IntervalTree from '@flatten-js/interval-tree';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
-export default class extends BaseFeatureDataAdapter {
-    protected gffFeatures?: Promise<{
-        header: string;
-        intervalTree: Record<string, IntervalTree>;
-    }>;
-    private loadDataP;
-    private loadData;
-    getRefNames(opts?: BaseOptions): Promise<string[]>;
-    getHeader(): Promise<string>;
-    getFeatures(query: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    private featureData;
-    freeResources(): void;
-}
+import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { NoAssemblyRegion } from '@jbrowse/core/util/types';
+import IntervalTree from '@flatten-js/interval-tree';
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+export default class extends BaseFeatureDataAdapter {
+    protected gffFeatures?: Promise<{
+        header: string;
+        intervalTree: Record<string, IntervalTree>;
+    }>;
+    private loadDataP;
+    private loadData;
+    getRefNames(opts?: BaseOptions): Promise<string[]>;
+    getHeader(): Promise<string>;
+    getFeatures(query: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    private featureData;
+    freeResources(): void;
+}

package/dist/Gff3Adapter/Gff3Adapter.js

@@ -0,0 +1,402 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+
+var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
+
+var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+
+var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
+
+var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
+
+var _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
+
+var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));
+
+var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));
+
+var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
+
+var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
+
+var _BaseAdapter = require("@jbrowse/core/data_adapters/BaseAdapter");
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _io = require("@jbrowse/core/util/io");
+
+var _rxjs = require("@jbrowse/core/util/rxjs");
+
+var _intervalTree = _interopRequireDefault(require("@flatten-js/interval-tree"));
+
+var _simpleFeature = _interopRequireDefault(require("@jbrowse/core/util/simpleFeature"));
+
+var _bgzfFilehandle = require("@gmod/bgzf-filehandle");
+
+var _gff = _interopRequireDefault(require("@gmod/gff"));
+
+function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
+
+function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2["default"])(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
+
+function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2["default"])(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = (0, _getPrototypeOf2["default"])(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return (0, _possibleConstructorReturn2["default"])(this, result); }; }
+
+function _isNativeReflectConstruct() { if (typeof Reflect === "undefined" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === "function") return true; try { Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {})); return true; } catch (e) { return false; } }
+
+function isGzip(buf) {
+  return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
+}
+
+var _default = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
+  (0, _inherits2["default"])(_default, _BaseFeatureDataAdapt);
+
+  var _super = _createSuper(_default);
+
+  function _default() {
+    var _this;
+
+    (0, _classCallCheck2["default"])(this, _default);
+
+    for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
+      args[_key] = arguments[_key];
+    }
+
+    _this = _super.call.apply(_super, [this].concat(args));
+    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "gffFeatures", void 0);
+    return _this;
+  }
+
+  (0, _createClass2["default"])(_default, [{
+    key: "loadDataP",
+    value: function () {
+      var _loadDataP = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+        var _this2 = this;
+
+        var buffer, buf, data, lines, headerLines, i, header, feats, intervalTree;
+        return _regenerator["default"].wrap(function _callee$(_context) {
+          while (1) {
+            switch (_context.prev = _context.next) {
+              case 0:
+                _context.next = 2;
+                return (0, _io.openLocation)((0, _configuration.readConfObject)(this.config, 'gffLocation'), this.pluginManager).readFile();
+
+              case 2:
+                buffer = _context.sent;
+
+                if (!isGzip(buffer)) {
+                  _context.next = 9;
+                  break;
+                }
+
+                _context.next = 6;
+                return (0, _bgzfFilehandle.unzip)(buffer);
+
+              case 6:
+                _context.t0 = _context.sent;
+                _context.next = 10;
+                break;
+
+              case 9:
+                _context.t0 = buffer;
+
+              case 10:
+                buf = _context.t0;
+
+                if (!(buf.length > 536870888)) {
+                  _context.next = 13;
+                  break;
+                }
+
+                throw new Error('Data exceeds maximum string length (512MB)');
+
+              case 13:
+                data = new TextDecoder('utf8', {
+                  fatal: true
+                }).decode(buf);
+                lines = data.split('\n');
+                headerLines = [];
+
+                for (i = 0; i < lines.length && lines[i].startsWith('#'); i++) {
+                  headerLines.push(lines[i]);
+                }
+
+                header = headerLines.join('\n');
+                feats = _gff["default"].parseStringSync(data, {
+                  parseFeatures: true,
+                  parseComments: false,
+                  parseDirectives: false,
+                  parseSequences: false
+                });
+                intervalTree = feats.flat().map(function (f, i) {
+                  return new _simpleFeature["default"]({
+                    data: _this2.featureData(f),
+                    id: "".concat(_this2.id, "-offset-").concat(i)
+                  });
+                }).reduce(function (acc, obj) {
+                  var key = obj.get('refName');
+
+                  if (!acc[key]) {
+                    acc[key] = new _intervalTree["default"]();
+                  }
+
+                  acc[key].insert([obj.get('start'), obj.get('end')], obj);
+                  return acc;
+                }, {});
+                return _context.abrupt("return", {
+                  header: header,
+                  intervalTree: intervalTree
+                });
+
+              case 21:
+              case "end":
+                return _context.stop();
+            }
+          }
+        }, _callee, this);
+      }));
+
+      function loadDataP() {
+        return _loadDataP.apply(this, arguments);
+      }
+
+      return loadDataP;
+    }()
+  }, {
+    key: "loadData",
+    value: function () {
+      var _loadData = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2() {
+        var _this3 = this;
+
+        return _regenerator["default"].wrap(function _callee2$(_context2) {
+          while (1) {
+            switch (_context2.prev = _context2.next) {
+              case 0:
+                if (!this.gffFeatures) {
+                  this.gffFeatures = this.loadDataP()["catch"](function (e) {
+                    _this3.gffFeatures = undefined;
+                    throw e;
+                  });
+                }
+
+                return _context2.abrupt("return", this.gffFeatures);
+
+              case 2:
+              case "end":
+                return _context2.stop();
+            }
+          }
+        }, _callee2, this);
+      }));
+
+      function loadData() {
+        return _loadData.apply(this, arguments);
+      }
+
+      return loadData;
+    }()
+  }, {
+    key: "getRefNames",
+    value: function () {
+      var _getRefNames = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee3() {
+        var opts,
+            _yield$this$loadData,
+            intervalTree,
+            _args3 = arguments;
+
+        return _regenerator["default"].wrap(function _callee3$(_context3) {
+          while (1) {
+            switch (_context3.prev = _context3.next) {
+              case 0:
+                opts = _args3.length > 0 && _args3[0] !== undefined ? _args3[0] : {};
+                _context3.next = 3;
+                return this.loadData();
+
+              case 3:
+                _yield$this$loadData = _context3.sent;
+                intervalTree = _yield$this$loadData.intervalTree;
+                return _context3.abrupt("return", Object.keys(intervalTree));
+
+              case 6:
+              case "end":
+                return _context3.stop();
+            }
+          }
+        }, _callee3, this);
+      }));
+
+      function getRefNames() {
+        return _getRefNames.apply(this, arguments);
+      }
+
+      return getRefNames;
+    }()
+  }, {
+    key: "getHeader",
+    value: function () {
+      var _getHeader = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee4() {
+        var _yield$this$loadData2, header;
+
+        return _regenerator["default"].wrap(function _callee4$(_context4) {
+          while (1) {
+            switch (_context4.prev = _context4.next) {
+              case 0:
+                _context4.next = 2;
+                return this.loadData();
+
+              case 2:
+                _yield$this$loadData2 = _context4.sent;
+                header = _yield$this$loadData2.header;
+                return _context4.abrupt("return", header);
+
+              case 5:
+              case "end":
+                return _context4.stop();
+            }
+          }
+        }, _callee4, this);
+      }));
+
+      function getHeader() {
+        return _getHeader.apply(this, arguments);
+      }
+
+      return getHeader;
+    }()
+  }, {
+    key: "getFeatures",
+    value: function getFeatures(query) {
+      var _this4 = this;
+
+      var opts = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};
+      return (0, _rxjs.ObservableCreate)( /*#__PURE__*/function () {
+        var _ref = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee5(observer) {
+          var _intervalTree$refName, start, end, refName, _yield$_this4$loadDat, intervalTree;
+
+          return _regenerator["default"].wrap(function _callee5$(_context5) {
+            while (1) {
+              switch (_context5.prev = _context5.next) {
+                case 0:
+                  _context5.prev = 0;
+                  start = query.start, end = query.end, refName = query.refName;
+                  _context5.next = 4;
+                  return _this4.loadData();
+
+                case 4:
+                  _yield$_this4$loadDat = _context5.sent;
+                  intervalTree = _yield$_this4$loadDat.intervalTree;
+                  (_intervalTree$refName = intervalTree[refName]) === null || _intervalTree$refName === void 0 ? void 0 : _intervalTree$refName.search([start, end]).forEach(function (f) {
+                    return observer.next(f);
+                  });
+                  observer.complete();
+                  _context5.next = 13;
+                  break;
+
+                case 10:
+                  _context5.prev = 10;
+                  _context5.t0 = _context5["catch"](0);
+                  observer.error(_context5.t0);
+
+                case 13:
+                case "end":
+                  return _context5.stop();
+              }
+            }
+          }, _callee5, null, [[0, 10]]);
+        }));
+
+        return function (_x) {
+          return _ref.apply(this, arguments);
+        };
+      }(), opts.signal);
+    }
+  }, {
+    key: "featureData",
+    value: function featureData(data) {
+      var _this5 = this;
+
+      var f = _objectSpread({}, data);
+
+      f.start -= 1; // convert to interbase
+
+      if (data.strand === '+') {
+        f.strand = 1;
+      } else if (data.strand === '-') {
+        f.strand = -1;
+      } else if (data.strand === '.') {
+        f.strand = 0;
+      } else {
+        f.strand = undefined;
+      }
+
+      f.phase = Number(data.phase);
+      f.refName = data.seq_id;
+
+      if (data.score === null) {
+        delete f.score;
+      }
+
+      if (data.phase === null) {
+        delete f.score;
+      }
+
+      var defaultFields = ['start', 'end', 'seq_id', 'score', 'type', 'source', 'phase', 'strand'];
+      var dataAttributes = data.attributes || {};
+      Object.keys(dataAttributes).forEach(function (a) {
+        var b = a.toLowerCase();
+
+        if (defaultFields.includes(b)) {
+          // add "suffix" to tag name if it already exists
+          // reproduces behavior of NCList
+          b += '2';
+        }
+
+        if (dataAttributes[a] !== null) {
+          var attr = dataAttributes[a];
+
+          if (Array.isArray(attr) && attr.length === 1) {
+            ;
+            var _attr = attr;
+
+            var _attr2 = (0, _slicedToArray2["default"])(_attr, 1);
+
+            attr = _attr2[0];
+          }
+
+          f[b] = attr;
+        }
+      });
+      f.refName = f.seq_id; // the SimpleFeature constructor takes care of recursively inflating subfeatures
+
+      if (data.child_features && data.child_features.length) {
+        f.subfeatures = data.child_features.map(function (childLocs) {
+          return childLocs.map(function (childLoc) {
+            return _this5.featureData(childLoc);
+          });
+        }).flat();
+      }
+
+      delete f.child_features;
+      delete f.data;
+      delete f.derived_features;
+      delete f.attributes;
+      delete f.seq_id;
+      return f;
+    }
+  }, {
+    key: "freeResources",
+    value: function
+      /* { region } */
+    freeResources() {}
+  }]);
+  return _default;
+}(_BaseAdapter.BaseFeatureDataAdapter);
+
+exports["default"] = _default;

package/dist/Gff3Adapter/Gff3Adapter.test.js

@@ -0,0 +1,71 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+
+var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+
+var _operators = require("rxjs/operators");
+
+var _configSchema = _interopRequireDefault(require("./configSchema"));
+
+var _Gff3Adapter = _interopRequireDefault(require("./Gff3Adapter"));
+
+var _webEncoding = require("web-encoding");
+
+window.TextDecoder = _webEncoding.TextDecoder;
+describe('adapter can fetch features from volvox.gff3', function () {
+  var adapter;
+  beforeEach(function () {
+    adapter = new _Gff3Adapter["default"](_configSchema["default"].create({
+      gffLocation: {
+        localPath: require.resolve('../test_data/volvox.sort.gff3')
+      }
+    }));
+  });
+  it('test getfeatures on gff plain text adapter', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+    var features, featuresArray, featuresJsonArray;
+    return _regenerator["default"].wrap(function _callee$(_context) {
+      while (1) {
+        switch (_context.prev = _context.next) {
+          case 0:
+            features = adapter.getFeatures({
+              refName: 'ctgB',
+              start: 0,
+              end: 200000
+            });
+            _context.t0 = expect;
+            _context.next = 4;
+            return adapter.hasDataForRefName('ctgA');
+
+          case 4:
+            _context.t1 = _context.sent;
+            (0, _context.t0)(_context.t1).toBe(true);
+            _context.t2 = expect;
+            _context.next = 9;
+            return adapter.hasDataForRefName('ctgB');
+
+          case 9:
+            _context.t3 = _context.sent;
+            (0, _context.t2)(_context.t3).toBe(true);
+            _context.next = 13;
+            return features.pipe((0, _operators.toArray)()).toPromise();
+
+          case 13:
+            featuresArray = _context.sent;
+            // There are only 4 features in ctgB
+            expect(featuresArray.length).toBe(4);
+            featuresJsonArray = featuresArray.map(function (f) {
+              return f.toJSON();
+            });
+            expect(featuresJsonArray).toMatchSnapshot();
+
+          case 17:
+          case "end":
+            return _context.stop();
+        }
+      }
+    }, _callee);
+  })));
+});

package/dist/Gff3Adapter/configSchema.d.ts

@@ -1,2 +1,2 @@
-declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export default _default;
+declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/dist/Gff3Adapter/configSchema.js

@@ -0,0 +1,22 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _default = (0, _configuration.ConfigurationSchema)('Gff3Adapter', {
+  gffLocation: {
+    type: 'fileLocation',
+    defaultValue: {
+      uri: '/path/to/my.gff',
+      locationType: 'UriLocation'
+    }
+  }
+}, {
+  explicitlyTyped: true
+});
+
+exports["default"] = _default;

package/dist/Gff3Adapter/index.d.ts

@@ -1 +1 @@
-export { default as configSchema } from './configSchema';
+export { default as configSchema } from './configSchema';

package/dist/Gff3Adapter/index.js

@@ -0,0 +1,15 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+Object.defineProperty(exports, "configSchema", {
+  enumerable: true,
+  get: function get() {
+    return _configSchema["default"];
+  }
+});
+
+var _configSchema = _interopRequireDefault(require("./configSchema"));

package/dist/Gff3TabixAdapter/Gff3TabixAdapter.d.ts

@@ -1,20 +1,20 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
-import { TabixIndexedFile } from '@gmod/tabix';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
-export default class extends BaseFeatureDataAdapter {
-    protected gff: TabixIndexedFile;
-    protected dontRedispatch: string[];
-    constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
-    getRefNames(opts?: BaseOptions): Promise<any>;
-    getHeader(): Promise<string>;
-    getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    private getFeaturesHelper;
-    private parseLine;
-    private formatFeatures;
-    private featureData;
-    freeResources(): void;
-}
+import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { Region } from '@jbrowse/core/util/types';
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { TabixIndexedFile } from '@gmod/tabix';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import PluginManager from '@jbrowse/core/PluginManager';
+import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+export default class extends BaseFeatureDataAdapter {
+    protected gff: TabixIndexedFile;
+    protected dontRedispatch: string[];
+    constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
+    getRefNames(opts?: BaseOptions): Promise<any>;
+    getHeader(): Promise<string>;
+    getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    private getFeaturesHelper;
+    private parseLine;
+    private formatFeatures;
+    private featureData;
+    freeResources(): void;
+}