@jbrowse/plugin-gtf 1.7.11 → 2.0.0

package/esm/util.d.ts

@@ -0,0 +1,15 @@
+export declare type Strand = '+' | '-' | '.' | '?';
+export interface FeatureLoc {
+    [key: string]: unknown;
+    start: number;
+    end: number;
+    strand: Strand;
+    seq_name: string;
+    child_features: FeatureLoc[][];
+    data: unknown;
+    derived_features: unknown;
+    attributes: {
+        [key: string]: unknown[];
+    };
+}
+export declare function featureData(data: FeatureLoc): Record<string, unknown>;

package/esm/util.js

@@ -0,0 +1,62 @@
+export function featureData(data) {
+    const f = { ...data };
+    f.start -= 1; // convert to interbase
+    f.strand = { '+': 1, '-': -1, '.': 0, '?': undefined }[data.strand]; // convert strand
+    f.phase = Number(data.frame);
+    f.refName = data.seq_name;
+    if (data.score === null) {
+        delete f.score;
+    }
+    if (data.frame === null) {
+        delete f.score;
+    }
+    const defaultFields = [
+        'start',
+        'end',
+        'seq_name',
+        'score',
+        'featureType',
+        'source',
+        'frame',
+        'strand',
+    ];
+    Object.keys(data.attributes).forEach(a => {
+        let b = a.toLowerCase();
+        if (defaultFields.includes(b)) {
+            // add "suffix" to tag name if it already exists
+            // reproduces behavior of NCList
+            b += '2';
+        }
+        if (data.attributes[a] !== null) {
+            let attr = data.attributes[a];
+            if (Array.isArray(attr) && attr.length === 1) {
+                // gtf uses double quotes for text values in the attributes column, remove them
+                const formattedAttr = attr[0].replace(/^"|"$/g, '');
+                attr = formattedAttr;
+            }
+            f[b] = attr;
+        }
+    });
+    f.refName = f.seq_name;
+    f.type = f.featureType;
+    // the SimpleFeature constructor takes care of recursively inflating subfeatures
+    if (data.child_features && data.child_features.length) {
+        f.subfeatures = data.child_features
+            .map(childLocs => childLocs.map(childLoc => featureData(childLoc)))
+            .flat();
+    }
+    delete f.child_features;
+    delete f.data;
+    delete f.derived_features;
+    // eslint-disable-next-line no-underscore-dangle
+    delete f._linehash;
+    delete f.attributes;
+    delete f.seq_name;
+    delete f.featureType;
+    delete f.frame;
+    if (f.transcript_id) {
+        f.name = f.transcript_id;
+    }
+    return f;
+}
+//# sourceMappingURL=util.js.map

package/esm/util.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-gtf",
-  "version": "1.7.11",
+  "version": "2.0.0",
   "description": "JBrowse 2 gtf feature adapter",
   "keywords": [
     "jbrowse",
@@ -20,17 +20,21 @@
   "main": "dist/index.js",
   "files": [
     "dist",
-    "src"
+    "src",
+    "esm"
   ],
   "scripts": {
-    "build": "babel src --root-mode upward --out-dir dist --extensions .ts,.js,.tsx,.jsx",
+    "build": "npm-run-all build:*",
     "test": "cd ../..; jest plugins/gtf --passWithNoTests",
     "prepublishOnly": "yarn test",
     "prepack": "yarn build; yarn useDist",
     "postpack": "yarn useSrc",
     "useDist": "node ../../scripts/useDist.js",
     "useSrc": "node ../../scripts/useSrc.js",
-    "postbuild": "tsc --build tsconfig.build.json"
+    "prebuild": "npm run clean",
+    "build:esm": "tsc --build tsconfig.build.esm.json",
+    "build:es5": "tsc --build tsconfig.build.es5.json",
+    "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
     "@babel/runtime": "^7.17.9",
@@ -41,9 +45,10 @@
   "peerDependencies": {
     "@jbrowse/core": "^1.0.0",
     "@jbrowse/plugin-linear-genome-view": "^1.0.0",
-    "@material-ui/core": "^4.12.2",
-    "mobx-react": "^6.0.0",
-    "mobx-state-tree": "3.14.1",
+    "@mui/material": "^5.0.0",
+    "mobx": "^6.0.0",
+    "mobx-react": "^7.0.0",
+    "mobx-state-tree": "^5.0.0",
     "prop-types": "^15.0.0",
     "react": ">=16.8.0",
     "rxjs": "^6.0.0"
@@ -51,5 +56,8 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "5c21beb48a21f08b0091d293f09ac99174c48f77"
+  "distModule": "esm/index.js",
+  "srcModule": "src/index.ts",
+  "module": "esm/index.js",
+  "gitHead": "ecc7f5d47351a5ea04bc00f3a6eb6dfb607342e6"
 }

package/dist/GtfAdapter/GtfAdapter.test.js

@@ -1,127 +0,0 @@
-"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 _GtfAdapter = _interopRequireDefault(require("./GtfAdapter"));
-
-var _webEncoding = require("web-encoding");
-
-window.TextDecoder = _webEncoding.TextDecoder;
-describe('adapter can fetch features from volvox.sorted.gtf', function () {
-  var adapter;
-  beforeEach(function () {
-    adapter = new _GtfAdapter.default(_configSchema.default.create({
-      gtfLocation: {
-        localPath: require.resolve('../test_data/volvox.sorted.gtf')
-      }
-    }));
-  });
-  it('test getfeatures on gtf plain text adapter', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-    var features, featuresArray, featuresJsonArray;
-    return _regenerator.default.wrap(function _callee$(_context) {
-      while (1) {
-        switch (_context.prev = _context.next) {
-          case 0:
-            features = adapter.getFeatures({
-              refName: 'ctgA',
-              start: 0,
-              end: 100000
-            });
-            _context.t0 = expect;
-            _context.next = 4;
-            return adapter.hasDataForRefName('ctgA');
-
-          case 4:
-            _context.t1 = _context.sent;
-            (0, _context.t0)(_context.t1).toBe(true);
-            _context.t2 = expect;
-            _context.next = 9;
-            return adapter.hasDataForRefName('ctgB');
-
-          case 9:
-            _context.t3 = _context.sent;
-            (0, _context.t2)(_context.t3).toBe(false);
-            _context.next = 13;
-            return features.pipe((0, _operators.toArray)()).toPromise();
-
-          case 13:
-            featuresArray = _context.sent;
-            // There are only 4 features in ctgB
-            expect(featuresArray.length).toBe(6);
-            featuresJsonArray = featuresArray.map(function (f) {
-              return f.toJSON();
-            });
-            expect(featuresJsonArray).toMatchSnapshot();
-
-          case 17:
-          case "end":
-            return _context.stop();
-        }
-      }
-    }, _callee);
-  })));
-});
-test('can instantiate new GtfAdapter and check for demo data', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
-  var demoAdapter, features, featuresArray, featuresJsonArray;
-  return _regenerator.default.wrap(function _callee2$(_context2) {
-    while (1) {
-      switch (_context2.prev = _context2.next) {
-        case 0:
-          demoAdapter = new _GtfAdapter.default(_configSchema.default.create({
-            gtfLocation: {
-              localPath: require.resolve('../test_data/demo.gtf')
-            }
-          }));
-          _context2.t0 = expect;
-          _context2.next = 4;
-          return demoAdapter.hasDataForRefName('GeneScaffold_1');
-
-        case 4:
-          _context2.t1 = _context2.sent;
-          (0, _context2.t0)(_context2.t1).toBe(true);
-          _context2.t2 = expect;
-          _context2.next = 9;
-          return demoAdapter.hasDataForRefName('GeneScaffold_10');
-
-        case 9:
-          _context2.t3 = _context2.sent;
-          (0, _context2.t2)(_context2.t3).toBe(true);
-          _context2.t4 = expect;
-          _context2.next = 14;
-          return demoAdapter.hasDataForRefName('GeneScaffold_11');
-
-        case 14:
-          _context2.t5 = _context2.sent;
-          (0, _context2.t4)(_context2.t5).toBe(false);
-          features = demoAdapter.getFeatures({
-            refName: 'GeneScaffold_1',
-            start: 0,
-            end: 1100000
-          });
-          _context2.next = 19;
-          return features.pipe((0, _operators.toArray)()).toPromise();
-
-        case 19:
-          featuresArray = _context2.sent;
-          featuresJsonArray = featuresArray.map(function (f) {
-            return f.toJSON();
-          }); // ENSVPAT00000000407
-
-          expect(featuresArray.length).toEqual(1);
-          expect(featuresJsonArray).toMatchSnapshot();
-
-        case 23:
-        case "end":
-          return _context2.stop();
-      }
-    }
-  }, _callee2);
-})));

package/dist/declare.d.js

@@ -1 +0,0 @@
-"use strict";