jbrowse-plugin-msaview 1.0.17 → 2.0.0

package/src/utils/msa.ts

@@ -0,0 +1,111 @@
+import { textfetch, timeout } from './fetch'
+
+const base = `https://www.ebi.ac.uk/Tools/services/rest`
+
+async function runClustalOmega({
+  sequence,
+  onProgress,
+}: {
+  sequence: string
+  onProgress: (arg: string) => void
+}) {
+  const jobId = await textfetch(`${base}/clustalo/run`, {
+    method: 'POST',
+    body: new URLSearchParams({
+      email: 'colin.diesh@gmail.com',
+      sequence,
+    }),
+  })
+  await wait({ jobId, algorithm: 'clustalo', onProgress })
+  return {
+    msa: await textfetch(`${base}/clustalo/result/${jobId}/aln-clustal_num`),
+    tree: await textfetch(`${base}/clustalo/result/${jobId}/phylotree`),
+  }
+}
+
+async function runMuscle({
+  sequence,
+  onProgress,
+}: {
+  sequence: string
+  onProgress: (arg: string) => void
+}) {
+  const jobId = await textfetch(`${base}/muscle/run`, {
+    method: 'POST',
+    body: new URLSearchParams({
+      email: 'colin.diesh@gmail.com',
+      format: 'clw',
+      tree: 'tree1',
+      sequence,
+    }),
+  })
+  await wait({ jobId, algorithm: 'muscle', onProgress })
+  return {
+    msa: await textfetch(`${base}/muscle/result/${jobId}/fa`),
+    tree: await textfetch(`${base}/muscle/result/${jobId}/phylotree`),
+  }
+}
+
+async function runKalign({
+  sequence,
+  onProgress,
+}: {
+  sequence: string
+  onProgress: (arg: string) => void
+}) {
+  const jobId = await textfetch(`${base}/kalign/run`, {
+    method: 'POST',
+    body: new URLSearchParams({
+      email: 'colin.diesh@gmail.com',
+      stype: 'protein',
+      sequence,
+    }),
+  })
+  await wait({ jobId, algorithm: 'kalign', onProgress })
+  return {
+    msa: await textfetch(`${base}/kalign/result/${jobId}/fa`),
+    tree: await textfetch(`${base}/kalign/result/${jobId}/phylotree`),
+  }
+}
+async function wait({
+  onProgress,
+  jobId,
+  algorithm,
+}: {
+  jobId: string
+  algorithm: string
+  onProgress: (arg: string) => void
+}) {
+  while (true) {
+    for (let i = 0; i < 10; i++) {
+      await timeout(1000)
+      onProgress(`Re-checking MSA status in... ${10 - i}`)
+    }
+    const result = await textfetch(`${base}/${algorithm}/status/${jobId}`)
+
+    if (result === 'FINISHED') {
+      break
+    }
+  }
+}
+
+export async function launchMSA({
+  algorithm,
+  sequence,
+  onProgress,
+}: {
+  algorithm: string
+  sequence: string
+  onProgress: (arg: string) => void
+}) {
+  onProgress(`Launching ${algorithm} MSA...`)
+  if (algorithm === 'clustalo') {
+    return runClustalOmega({ sequence, onProgress })
+  } else if (algorithm === 'muscle') {
+    return runMuscle({ sequence, onProgress })
+  } else if (algorithm === 'kalign') {
+    return runKalign({ sequence, onProgress })
+  } else {
+    throw new Error('unknown algorithm')
+  }
+}

package/src/utils/ncbiBlast.ts

@@ -0,0 +1,105 @@
+import { jsonfetch, textfetch, timeout } from './fetch'
+
+export const BLAST_URL = `https://blast.ncbi.nlm.nih.gov/blast/Blast.cgi`
+
+export async function queryBlast({
+  query,
+  blastDatabase,
+  blastProgram,
+  onProgress,
+  onRid,
+}: {
+  query: string
+  blastDatabase: string
+  blastProgram: string
+  onProgress: (arg: string) => void
+  onRid: (arg: string) => void
+}) {
+  onProgress('Submitting to NCBI BLAST...')
+  const { rid } = await initialQuery({
+    query,
+    blastDatabase,
+    blastProgram,
+  })
+  onRid(rid)
+  await waitForRid({ rid, onProgress })
+  const ret = await jsonfetch(
+    `${BLAST_URL}?CMD=Get&RID=${rid}&FORMAT_TYPE=JSON2_S&FORMAT_OBJECT=Alignment`,
+  )
+  const hits = ret.BlastOutput2[0].report.results.search.hits as {
+    description: { accession: string; id: string; sciname: string }[]
+    hsps: { hseq: string }[]
+  }[]
+
+  return { rid, hits }
+}
+
+async function initialQuery({
+  query,
+  blastProgram,
+  blastDatabase,
+}: {
+  query: string
+  blastProgram: string
+  blastDatabase: string
+}) {
+  const res = await textfetch(BLAST_URL, {
+    method: 'POST',
+    body: new URLSearchParams({
+      CMD: 'Put',
+      PROGRAM: blastProgram,
+      DATABASE: blastDatabase,
+      QUERY: query,
+      ...(blastDatabase === 'nr_clustered_seq'
+        ? {
+            CLUSTERED_DB: 'on',
+            DB_TYPE: 'Experimental Databases',
+          }
+        : {}),
+    }),
+  })
+
+  // the initial submission/query to the BLAST "REST API" does not return JSON
+  // as a response (e.g. FORMAT_TYPE=JSON does not work), so the RID is
+  // literally parsed from the text of the HTML that is returned
+  const rid = res.match(/^    RID = (.*$)/m)?.[1]
+  const rtoe = res.match(/^    RTOE = (.*$)/m)?.[1]
+
+  if (!rid) {
+    throw new Error('Failed to get RID from BLAST request')
+  }
+  return { rid, rtoe }
+}
+
+async function waitForRid({
+  rid,
+  onProgress,
+}: {
+  rid: string
+  onProgress: (arg: string) => void
+}) {
+  while (true) {
+    const iter = 20
+    for (let i = 0; i < iter; i++) {
+      await timeout(1000)
+      onProgress(`Re-checking BLAST status in... ${iter - i}`)
+    }
+
+    const res = await textfetch(
+      `${BLAST_URL}?CMD=Get&FORMAT_OBJECT=SearchInfo&RID=${rid}`,
+    )
+    if (res.match(/\s+Status=WAITING/m)) {
+      continue
+    } else if (res.match(/\s+Status=FAILED/m)) {
+      throw new Error(
+        `BLAST ${rid} failed; please report to blast-help@ncbi.nlm.nih.gov`,
+      )
+    } else if (res.match(/\s+Status=READY/m)) {
+      if (res.match(/\s+ThereAreHits=yes/m)) {
+        return true
+      } else {
+        throw new Error('No hits found')
+      }
+    }
+  }
+}

package/dist/config.json

@@ -1,8 +0,0 @@
-{
-  "plugins": [
-    {
-      "name": "MsaView",
-      "url": "https://unpkg.com/jbrowse-plugin-msaview/dist/jbrowse-plugin-msaview.umd.production.min.js"
-    }
-  ]
-}

package/dist/jbrowse-plugin-msaview.cjs.development.js

@@ -1,168 +0,0 @@
-'use strict';
-
-Object.defineProperty(exports, '__esModule', { value: true });
-
-function _interopDefault (ex) { return (ex && (typeof ex === 'object') && 'default' in ex) ? ex['default'] : ex; }
-
-var Plugin = _interopDefault(require('@jbrowse/core/Plugin'));
-var util = require('@jbrowse/core/util');
-var MSA = require('react-msaview');
-var ViewType = _interopDefault(require('@jbrowse/core/pluggableElementTypes/ViewType'));
-var GridOn = _interopDefault(require('@material-ui/icons/GridOn'));
-
-function _classCallCheck(instance, Constructor) {
-  if (!(instance instanceof Constructor)) {
-    throw new TypeError("Cannot call a class as a function");
-  }
-}
-
-function _defineProperties(target, props) {
-  for (var i = 0; i < props.length; i++) {
-    var descriptor = props[i];
-    descriptor.enumerable = descriptor.enumerable || false;
-    descriptor.configurable = true;
-    if ("value" in descriptor) descriptor.writable = true;
-    Object.defineProperty(target, descriptor.key, descriptor);
-  }
-}
-
-function _createClass(Constructor, protoProps, staticProps) {
-  if (protoProps) _defineProperties(Constructor.prototype, protoProps);
-  if (staticProps) _defineProperties(Constructor, staticProps);
-  return Constructor;
-}
-
-function _inherits(subClass, superClass) {
-  if (typeof superClass !== "function" && superClass !== null) {
-    throw new TypeError("Super expression must either be null or a function");
-  }
-
-  subClass.prototype = Object.create(superClass && superClass.prototype, {
-    constructor: {
-      value: subClass,
-      writable: true,
-      configurable: true
-    }
-  });
-  if (superClass) _setPrototypeOf(subClass, superClass);
-}
-
-function _getPrototypeOf(o) {
-  _getPrototypeOf = Object.setPrototypeOf ? Object.getPrototypeOf : function _getPrototypeOf(o) {
-    return o.__proto__ || Object.getPrototypeOf(o);
-  };
-  return _getPrototypeOf(o);
-}
-
-function _setPrototypeOf(o, p) {
-  _setPrototypeOf = Object.setPrototypeOf || function _setPrototypeOf(o, p) {
-    o.__proto__ = p;
-    return o;
-  };
-
-  return _setPrototypeOf(o, p);
-}
-
-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 _assertThisInitialized(self) {
-  if (self === void 0) {
-    throw new ReferenceError("this hasn't been initialised - super() hasn't been called");
-  }
-
-  return self;
-}
-
-function _possibleConstructorReturn(self, call) {
-  if (call && (typeof call === "object" || typeof call === "function")) {
-    return call;
-  } else if (call !== void 0) {
-    throw new TypeError("Derived constructors may only return object or undefined");
-  }
-
-  return _assertThisInitialized(self);
-}
-
-function _createSuper(Derived) {
-  var hasNativeReflectConstruct = _isNativeReflectConstruct();
-
-  return function _createSuperInternal() {
-    var Super = _getPrototypeOf(Derived),
-        result;
-
-    if (hasNativeReflectConstruct) {
-      var NewTarget = _getPrototypeOf(this).constructor;
-
-      result = Reflect.construct(Super, arguments, NewTarget);
-    } else {
-      result = Super.apply(this, arguments);
-    }
-
-    return _possibleConstructorReturn(this, result);
-  };
-}
-
-var version = "1.0.17";
-
-var MsaViewPlugin = /*#__PURE__*/function (_Plugin) {
-  _inherits(MsaViewPlugin, _Plugin);
-
-  var _super = /*#__PURE__*/_createSuper(MsaViewPlugin);
-
-  function MsaViewPlugin() {
-    var _this;
-
-    _classCallCheck(this, MsaViewPlugin);
-
-    _this = _super.apply(this, arguments);
-    _this.name = 'MsaViewPlugin';
-    _this.version = version;
-    return _this;
-  }
-
-  _createClass(MsaViewPlugin, [{
-    key: "install",
-    value: function install(pluginManager) {
-      console.log({
-        MSA: MSA
-      });
-      pluginManager.addViewType(function () {
-        return new ViewType({
-          name: 'MsaView',
-          //@ts-ignore
-          stateModel: MSA.MSAModel,
-          ReactComponent: MSA.MSAView
-        });
-      });
-    }
-  }, {
-    key: "configure",
-    value: function configure(pluginManager) {
-      if (util.isAbstractMenuManager(pluginManager.rootModel)) {
-        pluginManager.rootModel.appendToSubMenu(['Add'], {
-          label: 'Multiple sequence alignment view',
-          icon: GridOn,
-          onClick: function onClick(session) {
-            session.addView('MsaView', {});
-          }
-        });
-      }
-    }
-  }]);
-
-  return MsaViewPlugin;
-}(Plugin);
-
-exports.default = MsaViewPlugin;
-//# sourceMappingURL=jbrowse-plugin-msaview.cjs.development.js.map

package/dist/jbrowse-plugin-msaview.cjs.development.js.map

@@ -1 +0,0 @@
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package/dist/jbrowse-plugin-msaview.cjs.production.min.js

@@ -1,2 +0,0 @@
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-//# sourceMappingURL=jbrowse-plugin-msaview.cjs.production.min.js.map

package/dist/jbrowse-plugin-msaview.cjs.production.min.js.map

@@ -1 +0,0 @@
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package/dist/jbrowse-plugin-msaview.esm.js

@@ -1,163 +0,0 @@
-import Plugin from '@jbrowse/core/Plugin';
-import { isAbstractMenuManager } from '@jbrowse/core/util';
-import * as MSA from 'react-msaview';
-import { MSAModel, MSAView } from 'react-msaview';
-import ViewType from '@jbrowse/core/pluggableElementTypes/ViewType';
-import GridOn from '@material-ui/icons/GridOn';
-
-function _classCallCheck(instance, Constructor) {
-  if (!(instance instanceof Constructor)) {
-    throw new TypeError("Cannot call a class as a function");
-  }
-}
-
-function _defineProperties(target, props) {
-  for (var i = 0; i < props.length; i++) {
-    var descriptor = props[i];
-    descriptor.enumerable = descriptor.enumerable || false;
-    descriptor.configurable = true;
-    if ("value" in descriptor) descriptor.writable = true;
-    Object.defineProperty(target, descriptor.key, descriptor);
-  }
-}
-
-function _createClass(Constructor, protoProps, staticProps) {
-  if (protoProps) _defineProperties(Constructor.prototype, protoProps);
-  if (staticProps) _defineProperties(Constructor, staticProps);
-  return Constructor;
-}
-
-function _inherits(subClass, superClass) {
-  if (typeof superClass !== "function" && superClass !== null) {
-    throw new TypeError("Super expression must either be null or a function");
-  }
-
-  subClass.prototype = Object.create(superClass && superClass.prototype, {
-    constructor: {
-      value: subClass,
-      writable: true,
-      configurable: true
-    }
-  });
-  if (superClass) _setPrototypeOf(subClass, superClass);
-}
-
-function _getPrototypeOf(o) {
-  _getPrototypeOf = Object.setPrototypeOf ? Object.getPrototypeOf : function _getPrototypeOf(o) {
-    return o.__proto__ || Object.getPrototypeOf(o);
-  };
-  return _getPrototypeOf(o);
-}
-
-function _setPrototypeOf(o, p) {
-  _setPrototypeOf = Object.setPrototypeOf || function _setPrototypeOf(o, p) {
-    o.__proto__ = p;
-    return o;
-  };
-
-  return _setPrototypeOf(o, p);
-}
-
-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 _assertThisInitialized(self) {
-  if (self === void 0) {
-    throw new ReferenceError("this hasn't been initialised - super() hasn't been called");
-  }
-
-  return self;
-}
-
-function _possibleConstructorReturn(self, call) {
-  if (call && (typeof call === "object" || typeof call === "function")) {
-    return call;
-  } else if (call !== void 0) {
-    throw new TypeError("Derived constructors may only return object or undefined");
-  }
-
-  return _assertThisInitialized(self);
-}
-
-function _createSuper(Derived) {
-  var hasNativeReflectConstruct = _isNativeReflectConstruct();
-
-  return function _createSuperInternal() {
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-      result = Reflect.construct(Super, arguments, NewTarget);
-    } else {
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-    }
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-    return _possibleConstructorReturn(this, result);
-  };
-}
-
-var version = "1.0.17";
-
-var MsaViewPlugin = /*#__PURE__*/function (_Plugin) {
-  _inherits(MsaViewPlugin, _Plugin);
-
-  var _super = /*#__PURE__*/_createSuper(MsaViewPlugin);
-
-  function MsaViewPlugin() {
-    var _this;
-
-    _classCallCheck(this, MsaViewPlugin);
-
-    _this = _super.apply(this, arguments);
-    _this.name = 'MsaViewPlugin';
-    _this.version = version;
-    return _this;
-  }
-
-  _createClass(MsaViewPlugin, [{
-    key: "install",
-    value: function install(pluginManager) {
-      console.log({
-        MSA: MSA
-      });
-      pluginManager.addViewType(function () {
-        return new ViewType({
-          name: 'MsaView',
-          //@ts-ignore
-          stateModel: MSAModel,
-          ReactComponent: MSAView
-        });
-      });
-    }
-  }, {
-    key: "configure",
-    value: function configure(pluginManager) {
-      if (isAbstractMenuManager(pluginManager.rootModel)) {
-        pluginManager.rootModel.appendToSubMenu(['Add'], {
-          label: 'Multiple sequence alignment view',
-          icon: GridOn,
-          onClick: function onClick(session) {
-            session.addView('MsaView', {});
-          }
-        });
-      }
-    }
-  }]);
-
-  return MsaViewPlugin;
-}(Plugin);
-
-export default MsaViewPlugin;
-//# sourceMappingURL=jbrowse-plugin-msaview.esm.js.map

package/dist/jbrowse-plugin-msaview.esm.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"jbrowse-plugin-msaview.esm.js","sources":["../src/index.ts"],"sourcesContent":["import Plugin from '@jbrowse/core/Plugin'\nimport PluginManager from '@jbrowse/core/PluginManager'\nimport { version } from '../package.json'\nimport { AbstractSessionModel, isAbstractMenuManager } from '@jbrowse/core/util'\nimport * as MSA from 'react-msaview'\nimport ViewType from '@jbrowse/core/pluggableElementTypes/ViewType'\nimport GridOn from '@material-ui/icons/GridOn'\n\nexport default class MsaViewPlugin extends Plugin {\n  name = 'MsaViewPlugin'\n  version = version\n\n  install(pluginManager: PluginManager) {\n    console.log({ MSA })\n    pluginManager.addViewType(\n      () =>\n        new ViewType({\n          name: 'MsaView',\n          //@ts-ignore\n          stateModel: MSA.MSAModel,\n          ReactComponent: MSA.MSAView,\n        }),\n    )\n  }\n\n  configure(pluginManager: PluginManager) {\n    if (isAbstractMenuManager(pluginManager.rootModel)) {\n      pluginManager.rootModel.appendToSubMenu(['Add'], {\n        label: 'Multiple sequence alignment view',\n        icon: GridOn,\n        onClick: (session: AbstractSessionModel) => {\n          session.addView('MsaView', {})\n        },\n      })\n    }\n  }\n}\n"],"names":["MsaViewPlugin","version","pluginManager","console","log","MSA","addViewType","ViewType","name","stateModel","ReactComponent","isAbstractMenuManager","rootModel","appendToSubMenu","label","icon","GridOn","onClick","session","addView","Plugin"],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;IAQqBA;;;;;AAArB;;;;;;AACE,cAAA,GAAO,eAAP;AACA,iBAAA,GAAUC,OAAV;;AA0BD;;;;WAxBC,iBAAQC,aAAR;AACEC,MAAAA,OAAO,CAACC,GAAR,CAAY;AAAEC,QAAAA,GAAG,EAAHA;AAAF,OAAZ;AACAH,MAAAA,aAAa,CAACI,WAAd,CACE;AAAA,eACE,IAAIC,QAAJ,CAAa;AACXC,UAAAA,IAAI,EAAE,SADK;AAEX;AACAC,UAAAA,UAAU,EAAEJ,QAHD;AAIXK,UAAAA,cAAc,EAAEL;AAJL,SAAb,CADF;AAAA,OADF;AASD;;;WAED,mBAAUH,aAAV;AACE,UAAIS,qBAAqB,CAACT,aAAa,CAACU,SAAf,CAAzB,EAAoD;AAClDV,QAAAA,aAAa,CAACU,SAAd,CAAwBC,eAAxB,CAAwC,CAAC,KAAD,CAAxC,EAAiD;AAC/CC,UAAAA,KAAK,EAAE,kCADwC;AAE/CC,UAAAA,IAAI,EAAEC,MAFyC;AAG/CC,UAAAA,OAAO,EAAE,iBAACC,OAAD;AACPA,YAAAA,OAAO,CAACC,OAAR,CAAgB,SAAhB,EAA2B,EAA3B;AACD;AAL8C,SAAjD;AAOD;AACF;;;;EA3BwCC;;;;"}