genoverse 4.0.5 → 4.0.8

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Files changed (20) hide show
  1. package/README.md +5 -5
  2. package/dist/129.genoverse.js.map +1 -1
  3. package/dist/232.genoverse.js.map +1 -1
  4. package/dist/394.genoverse.js.map +1 -1
  5. package/dist/469.genoverse.js.map +1 -1
  6. package/dist/530.genoverse.js.map +1 -1
  7. package/dist/804.genoverse.js +1 -1
  8. package/dist/804.genoverse.js.map +1 -1
  9. package/dist/842.genoverse.js.map +1 -1
  10. package/dist/893.genoverse.js.map +1 -1
  11. package/dist/949.genoverse.js.map +1 -1
  12. package/dist/952.genoverse.js.map +1 -1
  13. package/dist/genoverse.js +1 -1
  14. package/dist/genoverse.js.map +1 -1
  15. package/index.html +2 -2
  16. package/package.json +4 -4
  17. package/src/js/Track/Model/Sequence/Fasta.js +1 -1
  18. package/src/js/Track/View/Gene/Ensembl.js +37 -19
  19. package/src/js/plugins/controlPanel.js +1 -1
  20. package/test/View/calculate-biotype-legend.test.js +28 -0
package/index.html CHANGED
@@ -14,7 +14,7 @@
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  </style>
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  </head>
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  <body>
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- <a class="fork" href="https://github.com/wtsi-web/Genoverse" target="_blank"><img src="https://s3.amazonaws.com/github/ribbons/forkme_right_orange_ff7600.png" alt="Fork me on GitHub"></a>
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+ <a class="fork" href="https://github.com/WTSI-decipher-grp/Genoverse" target="_blank"><img src="https://s3.amazonaws.com/github/ribbons/forkme_right_orange_ff7600.png" alt="Fork me on GitHub"></a>
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  <div class="container">
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  <div class="head"><h1>Genoverse - interactive HTML5 genome browser</h1></div>
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  <div class="wrap">
@@ -25,7 +25,7 @@
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  <p>Data is visualized in the browser, meaning Genoverse can be installed on any website and show data from a wide range of online or local sources.</p>
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  <p>Genoverse works with a variety of formats, such as XML, JSON, GFF, GFF3, BED (try drag-n-drop one), and can be customized to parse and display any data source as required.</p>
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- <p class="help">If you have any questions or need help, please raise an issue at <a href="https://github.com/wtsi-web/Genoverse" target="_blank">https://github.com/wtsi-web/Genoverse</a></p>
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+ <p class="help">If you have any questions or need help, please raise an issue at <a href="https://github.com/WTSI-decipher-grp/Genoverse" target="_blank">https://github.com/WTSI-decipher-grp/Genoverse</a></p>
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  </div>
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  </div>
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package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "genoverse",
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- "version": "4.0.5",
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+ "version": "4.0.8",
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  "description": "Genoverse is a portable, customizable, back-end independent JavaScript and HTML5 based genome browser which allows the user to explore data in a dynamic and interactive manner.",
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  "main": "src/js/Genoverse.js",
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  "directories": {
@@ -16,14 +16,14 @@
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  },
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  "repository": {
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  "type": "git",
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- "url": "git+https://github.com/wtsi-web/Genoverse.git"
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+ "url": "git+https://github.com/WTSI-decipher-grp/Genoverse.git"
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  },
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  "author": "Simon Brent",
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  "license": "BSD-3-Clause",
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  "bugs": {
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- "url": "https://github.com/wtsi-web/Genoverse/issues"
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+ "url": "https://github.com/WTSI-decipher-grp/Genoverse/issues"
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  },
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- "homepage": "https://wtsi-web.github.io/Genoverse/",
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+ "homepage": "https://wtsi-decipher-grp.github.io/Genoverse/",
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  "devDependencies": {
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  "@babel/core": "^7.17.2",
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  "@babel/eslint-parser": "^7.17.0",
package/src/js/Track/Model/Sequence/Fasta.js CHANGED
@@ -1,7 +1,7 @@
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  import Model from '../Sequence';
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  export default Model.extend({
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- url: 'https://wtsi-web.github.io/Genoverse/data/Homo_sapiens.GRCh37.72.dna.chromosome.1.fa', // Example url
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+ url: 'https://wtsi-decipher-grp.github.io/Genoverse/data/Homo_sapiens.GRCh37.72.dna.chromosome.1.fa', // Example url
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  // Following settings could be left undefined and will be detected automatically via .getStartByte()
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  startByte : undefined, // Byte in the file where the sequence actually starts
package/src/js/Track/View/Gene/Ensembl.js CHANGED
@@ -1,46 +1,64 @@
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  import View from '../Gene';
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+ /**
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+ * Provides a function setFeatureColor for defining the feature colour and legend label
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+ * for ensembl genes and transcripts based on their logic_name and biotype properties.
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+ *
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+ * Biotypes are defined in
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+ * https://www.ensembl.org/info/genome/genebuild/biotypes.html
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+ *
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+ * Ensembl colours are defined in
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+ * https://github.com/Ensembl/ensembl-webcode/blob/main/conf/ini-files/COLOUR.ini
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+ */
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+
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  export default View.extend({
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  setFeatureColor: function (feature) {
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  const processedTranscript = {
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- 'sense_intronic' : 1,
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- 'sense_overlapping' : 1,
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- 'processed_transcript' : 1,
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- 'nonsense_mediated_decay' : 1,
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- 'non_stop_decay' : 1,
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- 'antisense' : 1,
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- 'retained_intron' : 1,
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- 'tec' : 1,
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- 'non_coding' : 1,
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- 'ambiguous_orf' : 1,
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- 'disrupted_domain' : 1,
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- '3prime_overlapping_ncrna' : 1,
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+ 'sense_intronic' : 1,
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+ 'sense_overlapping' : 1,
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+ 'processed_transcript' : 1,
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+ 'nonsense_mediated_decay' : 1,
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+ 'non_stop_decay' : 1,
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+ 'antisense' : 1,
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+ 'retained_intron' : 1,
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+ 'tec' : 1,
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+ 'non_coding' : 1,
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+ 'ambiguous_orf' : 1,
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+ 'disrupted_domain' : 1,
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+ '3prime_overlapping_ncrna' : 1,
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+ 'protein_coding_CDS_not_defined' : 1, // new in e108
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  };
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  feature.color = '#000000';
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- if (feature.logic_name.indexOf('ensembl_havana') === 0) {
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+ const logicName = feature.logic_name || '';
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+ const biotype = (feature.biotype || '').toLowerCase();
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+
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+ if (logicName.indexOf('ensembl_havana') === 0) {
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  feature.color = '#CD9B1D';
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  feature.labelColor = '#B78000';
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  feature.legend = 'Merged Ensembl/Havana';
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- } else if (processedTranscript[feature.biotype.toLowerCase()]) {
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+ } else if (processedTranscript[biotype]) {
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  feature.color = '#0000FF';
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  feature.legend = 'Processed transcript';
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- } else if (feature.biotype === 'protein_coding') {
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+ } else if (feature.biotype.indexOf('protein_coding') > -1) {
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  feature.color = '#A00000';
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  feature.legend = 'Protein coding';
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- } else if (feature.biotype.indexOf('pseudogene') > -1) {
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+ } else if (feature.biotype === 'artifact' || biotype.indexOf('pseudogene') > -1) {
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  feature.color = '#666666';
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  feature.legend = 'Pseudogene';
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- } else if (/rna/i.test(feature.biotype) || feature.biotype === 'ribozyme') {
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+ } else if (/rna/.test(biotype) || biotype === 'ribozyme') {
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  feature.color = '#8B668B';
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  feature.legend = 'RNA gene';
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- } else if (/^tr_.+_gene$/i.test(feature.biotype)) {
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+ } else if (/^tr(?:_.+)?_gene$/.test(biotype)) {
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  feature.color = '#CD6600';
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  feature.legend = 'TR gene';
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- } else if (/^ig_.+_gene$/i.test(feature.biotype)) {
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+ } else if (/^ig_.+_gene$/.test(biotype)) {
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  feature.color = '#8B4500';
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  feature.legend = 'IG gene';
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+ } else if (biotype === 'lrg_gene') {
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+ feature.color = '#8080FF';
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+ feature.legend = 'LRG gene';
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  }
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  feature.labelColor = feature.labelColor || feature.color;
package/src/js/plugins/controlPanel.js CHANGED
@@ -349,7 +349,7 @@ const plugin = function (pluginConf) {
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  },
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  afterAddDomElements: function () {
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- this.wrapper.after('<div class="gv-powered-by">Powered by <a target="_blank" href="https://wtsi-web.github.io/Genoverse/">Genoverse</a></div>');
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+ this.wrapper.after('<div class="gv-powered-by">Powered by <a target="_blank" href="https://wtsi-decipher-grp.github.io/Genoverse/">Genoverse</a></div>');
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  this.superContainer.find('.gv-panel-left').append(this.labelContainer);
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  },
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package/test/View/calculate-biotype-legend.test.js ADDED
@@ -0,0 +1,28 @@
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+ const { $, Genoverse, afterTest } = require('../utils');
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+
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+ describe('All ensembl biotypes should be categorised by setFeatureColor:', () => {
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+ afterEach(afterTest);
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+
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+ // select * from (select distinct(biotype) from transcript union select distinct(biotype) from gene) biotypes order by biotype;
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+ const ensemblBiotypes = [ 'artifact', 'IG_C_gene', 'IG_C_pseudogene', 'IG_D_gene', 'IG_J_gene', 'IG_J_pseudogene', 'IG_pseudogene', 'IG_V_gene', 'IG_V_pseudogene', 'lncRNA', 'LRG_gene', 'miRNA', 'misc_RNA', 'Mt_rRNA', 'Mt_tRNA', 'nonsense_mediated_decay', 'non_stop_decay', 'processed_pseudogene', 'processed_transcript', 'protein_coding', 'protein_coding_LoF', 'pseudogene', 'retained_intron', 'ribozyme', 'rRNA', 'rRNA_pseudogene', 'scaRNA', 'scRNA', 'snoRNA', 'snRNA', 'sRNA', 'TEC', 'transcribed_processed_pseudogene', 'transcribed_unitary_pseudogene', 'transcribed_unprocessed_pseudogene', 'translated_processed_pseudogene', 'translated_unprocessed_pseudogene', 'TR_C_gene', 'TR_D_gene', 'TR_J_gene', 'TR_J_pseudogene', 'TR_V_gene', 'TR_V_pseudogene', 'unitary_pseudogene', 'unprocessed_pseudogene', 'vault_RNA' ];
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+
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+ ensemblBiotypes.forEach(
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+ biotype => it(
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+ `${biotype} should be categorised by setFeatureColor`, () => {
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+ const feature = { logic_name: '', biotype: biotype };
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+
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+ const [ track ] = new Genoverse({
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+ chr : 1,
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+ start : 1,
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+ end : 100,
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+ chromosomeSize : 100,
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+ tracks : [ Genoverse.Track.Gene.extend($.extend(true, {}, { data: [ feature ] })) ],
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+ }).tracks;
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+
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+ track.view.setFeatureColor(feature);
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+
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+ expect(feature.legend).toBeDefined();
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+ }
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+ )
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+ );
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+ });