@jbrowse/plugin-gff3 1.7.11 → 2.1.0

package/esm/Gff3TabixAdapter/Gff3TabixAdapter.js

@@ -0,0 +1,186 @@
+/* eslint-disable no-underscore-dangle */
+import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { doesIntersect2 } from '@jbrowse/core/util/range';
+import { openLocation } from '@jbrowse/core/util/io';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import SimpleFeature from '@jbrowse/core/util/simpleFeature';
+import { TabixIndexedFile } from '@gmod/tabix';
+import gff from '@gmod/gff';
+import { readConfObject, } from '@jbrowse/core/configuration';
+export default class extends BaseFeatureDataAdapter {
+    constructor(config, getSubAdapter, pluginManager) {
+        super(config, getSubAdapter, pluginManager);
+        const gffGzLocation = readConfObject(config, 'gffGzLocation');
+        const indexType = readConfObject(config, ['index', 'indexType']);
+        const location = readConfObject(config, ['index', 'location']);
+        const dontRedispatch = readConfObject(config, 'dontRedispatch');
+        this.dontRedispatch = dontRedispatch || ['chromosome', 'contig', 'region'];
+        this.gff = new TabixIndexedFile({
+            filehandle: openLocation(gffGzLocation, this.pluginManager),
+            csiFilehandle: indexType === 'CSI'
+                ? openLocation(location, this.pluginManager)
+                : undefined,
+            tbiFilehandle: indexType !== 'CSI'
+                ? openLocation(location, this.pluginManager)
+                : undefined,
+            chunkCacheSize: 50 * 2 ** 20,
+            renameRefSeqs: (n) => n,
+        });
+    }
+    async getRefNames(opts = {}) {
+        return this.gff.getReferenceSequenceNames(opts);
+    }
+    async getHeader() {
+        return this.gff.getHeader();
+    }
+    getFeatures(query, opts = {}) {
+        return ObservableCreate(async (observer) => {
+            const metadata = await this.gff.getMetadata();
+            this.getFeaturesHelper(query, opts, metadata, observer, true);
+        }, opts.signal);
+    }
+    async getFeaturesHelper(query, opts = {}, metadata, observer, allowRedispatch, originalQuery = query) {
+        try {
+            const lines = [];
+            await this.gff.getLines(query.refName, query.start, query.end, (line, fileOffset) => {
+                lines.push(this.parseLine(metadata.columnNumbers, line, fileOffset));
+            });
+            if (allowRedispatch && lines.length) {
+                let minStart = Infinity;
+                let maxEnd = -Infinity;
+                lines.forEach(line => {
+                    const featureType = line.fields[2];
+                    // only expand redispatch range if feature is not a "dontRedispatch" type
+                    // skips large regions like chromosome,region
+                    if (!this.dontRedispatch.includes(featureType)) {
+                        const start = line.start - 1; // gff is 1-based
+                        if (start < minStart) {
+                            minStart = start;
+                        }
+                        if (line.end > maxEnd) {
+                            maxEnd = line.end;
+                        }
+                    }
+                });
+                if (maxEnd > query.end || minStart < query.start) {
+                    // make a new feature callback to only return top-level features
+                    // in the original query range
+                    this.getFeaturesHelper({ ...query, start: minStart, end: maxEnd }, opts, metadata, observer, false, query);
+                    return;
+                }
+            }
+            const gff3 = lines
+                .map((lineRecord) => {
+                if (lineRecord.fields[8] && lineRecord.fields[8] !== '.') {
+                    if (!lineRecord.fields[8].includes('_lineHash')) {
+                        lineRecord.fields[8] += `;_lineHash=${lineRecord.lineHash}`;
+                    }
+                }
+                else {
+                    lineRecord.fields[8] = `_lineHash=${lineRecord.lineHash}`;
+                }
+                return lineRecord.fields.join('\t');
+            })
+                .join('\n');
+            const features = gff.parseStringSync(gff3, {
+                parseFeatures: true,
+                parseComments: false,
+                parseDirectives: false,
+                parseSequences: false,
+            });
+            features.forEach(featureLocs => this.formatFeatures(featureLocs).forEach(f => {
+                if (doesIntersect2(f.get('start'), f.get('end'), originalQuery.start, originalQuery.end)) {
+                    observer.next(f);
+                }
+            }));
+            observer.complete();
+        }
+        catch (e) {
+            observer.error(e);
+        }
+    }
+    parseLine(columnNumbers, line, fileOffset) {
+        const fields = line.split('\t');
+        // note: index column numbers are 1-based
+        return {
+            start: +fields[columnNumbers.start - 1],
+            end: +fields[columnNumbers.end - 1],
+            lineHash: fileOffset,
+            fields,
+        };
+    }
+    formatFeatures(featureLocs) {
+        return featureLocs.map(featureLoc => new SimpleFeature({
+            data: this.featureData(featureLoc),
+            // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
+            id: `${this.id}-offset-${featureLoc.attributes._lineHash[0]}`,
+        }));
+    }
+    featureData(data) {
+        const f = { ...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;
+        }
+        const defaultFields = [
+            'start',
+            'end',
+            'seq_id',
+            'score',
+            'type',
+            'source',
+            'phase',
+            'strand',
+        ];
+        const dataAttributes = data.attributes || {};
+        Object.keys(dataAttributes).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 (dataAttributes[a] !== null) {
+                let attr = dataAttributes[a];
+                if (Array.isArray(attr) && attr.length === 1) {
+                    ;
+                    [attr] = attr;
+                }
+                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(childLocs => childLocs.map(childLoc => this.featureData(childLoc)))
+                .flat();
+        }
+        delete f.child_features;
+        delete f.data;
+        delete f.derived_features;
+        delete f._linehash;
+        delete f.attributes;
+        delete f.seq_id;
+        return f;
+    }
+    freeResources( /* { region } */) { }
+}
+//# sourceMappingURL=Gff3TabixAdapter.js.map

package/esm/Gff3TabixAdapter/Gff3TabixAdapter.js.map

@@ -0,0 +1 @@
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package/esm/Gff3TabixAdapter/configSchema.d.ts

@@ -0,0 +1,2 @@
+declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/esm/Gff3TabixAdapter/configSchema.js

@@ -0,0 +1,27 @@
+import { types } from 'mobx-state-tree';
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+export default ConfigurationSchema('Gff3TabixAdapter', {
+    gffGzLocation: {
+        type: 'fileLocation',
+        defaultValue: { uri: '/path/to/my.gff.gz', locationType: 'UriLocation' },
+    },
+    index: ConfigurationSchema('Gff3TabixIndex', {
+        indexType: {
+            model: types.enumeration('IndexType', ['TBI', 'CSI']),
+            type: 'stringEnum',
+            defaultValue: 'TBI',
+        },
+        location: {
+            type: 'fileLocation',
+            defaultValue: {
+                uri: '/path/to/my.gff.gz.tbi',
+                locationType: 'UriLocation',
+            },
+        },
+    }),
+    dontRedispatch: {
+        type: 'stringArray',
+        defaultValue: ['chromosome', 'region'],
+    },
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/esm/Gff3TabixAdapter/configSchema.js.map

@@ -0,0 +1 @@
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package/esm/Gff3TabixAdapter/index.d.ts

@@ -0,0 +1 @@
+export { default as configSchema } from './configSchema';

package/esm/Gff3TabixAdapter/index.js

@@ -0,0 +1,2 @@
+export { default as configSchema } from './configSchema';
+//# sourceMappingURL=index.js.map

package/esm/Gff3TabixAdapter/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/Gff3TabixAdapter/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,gBAAgB,CAAA"}

package/esm/index.d.ts

@@ -0,0 +1,6 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+import Plugin from '@jbrowse/core/Plugin';
+export default class extends Plugin {
+    name: string;
+    install(pluginManager: PluginManager): void;
+}

package/esm/index.js

@@ -0,0 +1,62 @@
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
+import Plugin from '@jbrowse/core/Plugin';
+import { configSchema as gff3TabixAdapterConfigSchema } from './Gff3TabixAdapter';
+import { makeIndex, makeIndexType, getFileName, } from '@jbrowse/core/util/tracks';
+import { configSchema as gff3AdapterConfigSchema } from './Gff3Adapter';
+export default class extends Plugin {
+    constructor() {
+        super(...arguments);
+        this.name = 'GFF3Plugin';
+    }
+    install(pluginManager) {
+        pluginManager.addAdapterType(() => new AdapterType({
+            name: 'Gff3TabixAdapter',
+            configSchema: gff3TabixAdapterConfigSchema,
+            getAdapterClass: () => import('./Gff3TabixAdapter/Gff3TabixAdapter').then(r => r.default),
+        }));
+        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+            return (file, index, adapterHint) => {
+                const regexGuess = /\.gff3?\.b?gz$/i;
+                const adapterName = 'Gff3TabixAdapter';
+                const fileName = getFileName(file);
+                const indexName = index && getFileName(index);
+                if (regexGuess.test(fileName) || adapterHint === adapterName) {
+                    return {
+                        type: adapterName,
+                        bamLocation: file,
+                        gffGzLocation: file,
+                        index: {
+                            location: index || makeIndex(file, '.tbi'),
+                            indexType: makeIndexType(indexName, 'CSI', 'TBI'),
+                        },
+                    };
+                }
+                return adapterGuesser(file, index, adapterHint);
+            };
+        });
+        pluginManager.addAdapterType(() => new AdapterType({
+            name: 'Gff3Adapter',
+            configSchema: gff3AdapterConfigSchema,
+            getAdapterClass: () => import('./Gff3Adapter/Gff3Adapter').then(r => r.default),
+        }));
+        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+            return (file, index, adapterHint) => {
+                const regexGuess = /\.gff3?$/i;
+                const adapterName = 'Gff3Adapter';
+                const fileName = getFileName(file);
+                const obj = {
+                    type: adapterName,
+                    gffLocation: file,
+                };
+                if (regexGuess.test(fileName) && !adapterHint) {
+                    return obj;
+                }
+                else if (adapterHint === adapterName) {
+                    return obj;
+                }
+                return adapterGuesser(file, index, adapterHint);
+            };
+        });
+    }
+}
+//# sourceMappingURL=index.js.map

package/esm/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAEzE,OAAO,MAAM,MAAM,sBAAsB,CAAA;AACzC,OAAO,EAAE,YAAY,IAAI,4BAA4B,EAAE,MAAM,oBAAoB,CAAA;AAEjF,OAAO,EACL,SAAS,EACT,aAAa,EAEb,WAAW,GACZ,MAAM,2BAA2B,CAAA;AAClC,OAAO,EAAE,YAAY,IAAI,uBAAuB,EAAE,MAAM,eAAe,CAAA;AAEvE,MAAM,CAAC,OAAO,MAAO,SAAQ,MAAM;IAAnC;;QACE,SAAI,GAAG,YAAY,CAAA;IAyErB,CAAC;IAvEC,OAAO,CAAC,aAA4B;QAClC,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,WAAW,CAAC;YACd,IAAI,EAAE,kBAAkB;YACxB,YAAY,EAAE,4BAA4B;YAC1C,eAAe,EAAE,GAAG,EAAE,CACpB,MAAM,CAAC,qCAAqC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;SACrE,CAAC,CACL,CAAA;QACD,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,CAAC,cAA8B,EAAE,EAAE;YACjC,OAAO,CACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB,EACpB,EAAE;gBACF,MAAM,UAAU,GAAG,iBAAiB,CAAA;gBACpC,MAAM,WAAW,GAAG,kBAAkB,CAAA;gBACtC,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;gBAClC,MAAM,SAAS,GAAG,KAAK,IAAI,WAAW,CAAC,KAAK,CAAC,CAAA;gBAC7C,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,WAAW,KAAK,WAAW,EAAE;oBAC5D,OAAO;wBACL,IAAI,EAAE,WAAW;wBACjB,WAAW,EAAE,IAAI;wBACjB,aAAa,EAAE,IAAI;wBACnB,KAAK,EAAE;4BACL,QAAQ,EAAE,KAAK,IAAI,SAAS,CAAC,IAAI,EAAE,MAAM,CAAC;4BAC1C,SAAS,EAAE,aAAa,CAAC,SAAS,EAAE,KAAK,EAAE,KAAK,CAAC;yBAClD;qBACF,CAAA;iBACF;gBACD,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;YACjD,CAAC,CAAA;QACH,CAAC,CACF,CAAA;QACD,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,WAAW,CAAC;YACd,IAAI,EAAE,aAAa;YACnB,YAAY,EAAE,uBAAuB;YACrC,eAAe,EAAE,GAAG,EAAE,CACpB,MAAM,CAAC,2BAA2B,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;SAC3D,CAAC,CACL,CAAA;QACD,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,CAAC,cAA8B,EAAE,EAAE;YACjC,OAAO,CACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB,EACpB,EAAE;gBACF,MAAM,UAAU,GAAG,WAAW,CAAA;gBAC9B,MAAM,WAAW,GAAG,aAAa,CAAA;gBACjC,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;gBAClC,MAAM,GAAG,GAAG;oBACV,IAAI,EAAE,WAAW;oBACjB,WAAW,EAAE,IAAI;iBAClB,CAAA;gBACD,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,WAAW,EAAE;oBAC7C,OAAO,GAAG,CAAA;iBACX;qBAAM,IAAI,WAAW,KAAK,WAAW,EAAE;oBACtC,OAAO,GAAG,CAAA;iBACX;gBACD,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;YACjD,CAAC,CAAA;QACH,CAAC,CACF,CAAA;IACH,CAAC;CACF"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-gff3",
-  "version": "1.7.11",
+  "version": "2.1.0",
   "description": "JBrowse 2 gff3.",
   "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",
-    "postbuild": "tsc --build tsconfig.build.json",
+    "build": "npm-run-all build:*",
     "test": "cd ../..; jest plugins/gff3 --passWithNoTests",
     "prepublishOnly": "yarn test",
     "prepack": "yarn build; yarn useDist",
     "postpack": "yarn useSrc",
     "useDist": "node ../../scripts/useDist.js",
-    "useSrc": "node ../../scripts/useSrc.js"
+    "useSrc": "node ../../scripts/useSrc.js",
+    "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",
@@ -40,11 +44,12 @@
     "@gmod/tabix": "^1.5.2"
   },
   "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",
+    "@jbrowse/core": "^2.0.0",
+    "@jbrowse/plugin-linear-genome-view": "^2.0.0",
+    "@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"
@@ -52,5 +57,8 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "5c21beb48a21f08b0091d293f09ac99174c48f77"
+  "distModule": "esm/index.js",
+  "srcModule": "src/index.ts",
+  "module": "esm/index.js",
+  "gitHead": "0db0462fa1f9f15ab4869da085bcab032b9483c3"
 }

package/dist/Gff3Adapter/Gff3Adapter.test.js

@@ -1,71 +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 _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/Gff3TabixAdapter/Gff3TabixAdapter.test.js

@@ -1,74 +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 _Gff3TabixAdapter = _interopRequireDefault(require("./Gff3TabixAdapter"));
-
-describe('adapter can fetch features from volvox.gff3', function () {
-  var adapter;
-  beforeEach(function () {
-    adapter = new _Gff3TabixAdapter.default(_configSchema.default.create({
-      gffGzLocation: {
-        localPath: require.resolve('../test_data/volvox.sort.gff3.gz')
-      },
-      index: {
-        location: {
-          localPath: require.resolve('../test_data/volvox.sort.gff3.gz.tbi')
-        }
-      }
-    }));
-  });
-  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,
-              assemblyName: 'volvox'
-            });
-            _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);
-  })));
-});