* Add script to create an igv genome config from a hub.txt file

* general cleanup
igvteam · Jul 24, 2024 · 530dd97 · 530dd97
1 parent 27e2afa
commit 530dd97
Show file tree

Hide file tree

Showing 7 changed files with 50 additions and 102 deletions.
diff --git a/dev/ucsc/genome.html b/dev/ucsc/genome.html
@@ -6,76 +6,19 @@
 
 <body>
 
-<select id="select">
-    <option value=""></option>
-    <option value="https://hgdownload.soe.ucsc.edu/hubs/GCF/000/186/305/GCF_000186305.1/hub.txt">Many chromosomes ~ same
-        size
-    </option>
-    <option value="https://hgdownload.soe.ucsc.edu/hubs/GCA/022/747/635/GCA_022747635.1/hub.txt">Many chromosomes -
-        gradually decreasing
-        chromosomes
-    </option>
-    <option value="https://hgdownload.soe.ucsc.edu/hubs/GCF/013/103/735/GCF_013103735.1/hub.txt">24 large chromosomes
-    </option>
-    <option value="">T2T</option>
-</select>
-
-<label>
-    Enter full URL to hub.txt file
-    <input id="hub-input" type="text" style="width: 600px">
-</label>
-
-<button id="load-genome">Load hub as genome</button>
-<button id="load-session">Load hub as session</button>
-
-<br>
-<button id="dump-session">Dump session</button>
-
 <div id="igvDiv" style="padding-top: 50px;padding-bottom: 20px; height: auto"></div>
 
 <script type="module">
 
     import igv from "../../js/index.js"
-    import Hub from "../../js/ucsc/ucscHub.js"
-
-
-    const hubOptions = {
-        includeTracks: true
-    }
 
-    const hub = await Hub.loadHub("https://hgdownload.soe.ucsc.edu/hubs/GCF/002/006/095/GCF_002006095.1/hub.txt", hubOptions)
-
-    const igvConfig = {
-        reference: hub.getGenomeConfig(),
-        listeners: {
-            'genomechange': ({genome, trackConfigurations}) => {
-                console.log('genomechange')
-                console.log(genome)
-                console.log(trackConfigurations)
-            }
-        }
+   const igvConfig = {
+        genome: "GCA_000002305.1"
     }
 
 
     const browser = await igv.createBrowser(document.getElementById('igvDiv'), igvConfig)
 
-
-    const selector = document.getElementById("select")
-    selector.addEventListener("change", () => document.getElementById("hub-input").value = selector.value)
-
-    document.getElementById("hub-input").value = "https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/hub.txt"
-
-    document.getElementById("load-genome").addEventListener("click", async () => {
-        await browser.loadGenome({url: document.getElementById("hub-input").value})
-    })
-
-    document.getElementById("load-session").addEventListener("click", () =>
-        browser.loadSession({url: document.getElementById("hub-input").value}))
-
-    document.getElementById("dump-session").addEventListener("click", () => {
-        console.log(browser.toJSON())
-    })
-
 </script>
 
 </body>

diff --git a/js/browser.js b/js/browser.js
@@ -1467,13 +1467,6 @@ class Browser {
         return this.trackViews.map(tv => tv.track).filter(t => t !== undefined)
     }
 
-    getTrackURLs() {
-        return new Set(this.tracks
-            .filter(track => track.config && StringUtils.isString(track.config.url))
-            .map(track => track.config.url))
-    }
-
-
     /**
      * Set the track height globally for all tracks.  (Note: Its not clear why this is useful).
      * @param newHeight

diff --git a/js/feature/wigTrack.js b/js/feature/wigTrack.js
@@ -241,7 +241,7 @@ class WigTrack extends TrackBase {
                         }
 
                     } else {
-
+                        // Default graph type (bar)
                         const height = Math.min(pixelHeight, y - y0)
                         IGVGraphics.fillRect(ctx, x, y0, width, height, {fillStyle: color})
                         if (f.value > this.dataRange.max) {

diff --git a/js/ucsc/ucscHub.js b/js/ucsc/ucscHub.js
@@ -5,7 +5,6 @@
  https://genome.ucsc.edu/goldenpath/help/trackDb/trackDbHub.html
  */
 
-import {igvxhr} from "../../node_modules/igv-utils/src/index.js"
 
 class Hub {
 
@@ -110,7 +109,7 @@ transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/186/305/GCF_000186305.1
 isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/186/305/GCF_000186305.1
  */
 
-    getGenomeConfig(includeTrackGroups = "all") {
+    getGenomeConfig(options = {}) {
         // TODO -- add blat?  htmlPath?
 
         const id = this.genomeStanza.getProperty("genome")
@@ -156,11 +155,11 @@ isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/186/305/GCF_000186305.1
         if (this.genomeStanza.hasProperty("twoBitBptUrl")) {
             config.twoBitBptURL = this.baseURL + this.genomeStanza.getProperty("twoBitBptUrl")
         }
-        // chromSizes can take a very long time to load, and is not useful with the default WGV = off
-        // if (this.genomeStanza.hasProperty("chromSizes")) {
-        //     config.chromSizes = this.baseURL + this.genomeStanza.getProperty("chromSizes")
-        // }
 
+        // chromSizes can take a very long time to load, and is not useful with the default WGV = off
+        if (options.includeChromSizes && this.genomeStanza.hasProperty("chromSizes")) {
+            config.chromSizesURL = this.baseURL + this.genomeStanza.getProperty("chromSizes")
+        }
 
         if (this.hubStanza.hasProperty("longLabel")) {
             config.description = this.hubStanza.getProperty("longLabel").replace("/", "\n")
@@ -196,13 +195,10 @@ isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/186/305/GCF_000186305.1
             config.cytobandBbURL = this.baseURL + cytoStanza[0].getProperty("bigDataUrl")
         }
 
-        // Tracks.  To prevent loading tracks set `includeTrackGroups`to false or "none"
-        if (includeTrackGroups && "none" !== includeTrackGroups) {
-            const filter = (t) => !Hub.filterTracks.has(t.name) &&
-                "hide" !== t.getProperty("visibility") &&
-                ("all" === includeTrackGroups || t.getProperty("group") === includeTrackGroups)
-            config.tracks = this.#getTracksConfigs(filter)
-        }
+        // Tracks.
+        const filter = (t) => !Hub.filterTracks.has(t.name) && "hide" !== t.getProperty("visibility")
+        config.tracks = this.#getTracksConfigs(filter)
+
 
         return config
     }
@@ -430,7 +426,8 @@ class Stanza {
  */
 async function loadStanzas(url) {
 
-    const data = await igvxhr.loadString(url)
+    const response = await fetch(url)
+    const data = await response.text()
     const lines = data.split(/\n|\r\n|\r/g)
 
     const nodes = []

diff --git a/scripts/embedCssTemplate.js b/scripts/embedCssTemplate.js
diff --git a/scripts/hubToGenomeConfig.js b/scripts/hubToGenomeConfig.js
@@ -0,0 +1,36 @@
+/**
+ * Creates an IGV genome configuration json from a UCSC genark assembly hub.  It might also work with other
+ * UCSC hubs but has not been tested.
+ *
+ * Example use
+ * node hubToGenomeConfig.js GCF_002006095.1
+ * node hubToGenomeConfig.js https://hgdownload.soe.ucsc.edu/hubs/GCF/002/006/095/GCF_002006095.1/hub.txt
+ */
+
+import Hub from "../js/ucsc/ucscHub.js"
+import {convertToHubURL} from "../js/ucsc/ucscUtils.js"
+
+if (process.argv.length !== 3) {
+    console.log("Usage: node hubToGenomeConfig.js <hub accession or url to hub.text>")
+}
+
+const hubAccensionOrURL = process.argv[2]
+
+let url
+if (hubAccensionOrURL.startsWith("http://") || hubAccensionOrURL.startsWith("https://")) {
+    url = hubAccensionOrURL
+} else {
+    url = convertToHubURL(hubAccensionOrURL)
+}
+
+if (!url) {
+    console.error(`Could not convert input "${hubAccensionOrURL}" to genark hub url`)
+
+}
+
+const hub = await Hub.loadHub(url)
+
+const config = hub.getGenomeConfig({includeChromSizes: true})
+
+process.stdout.write(JSON.stringify(config, null, 2))
+
diff --git a/scripts/updateVersion.cjs b/scripts/updateVersion.cjs
@@ -4,23 +4,6 @@ const pj = require.resolve('../package.json');
 const jsonText = fs.readFileSync(pj, 'utf-8');
 const version = JSON.parse(jsonText).version;
 
-
-// Try to get git commit hash
-// let githash = "";
-// try {
-//     const headPath = require.resolve('../.git/HEAD');
-//     const rev = fs.readFileSync(headPath).toString().trim().split(/.*[: ]/).slice(-1)[0];
-//     if (rev.indexOf('/') === -1) {
-//         githash = rev;
-//     } else {
-//         const revpath = require.resolve('../.git/' + rev);
-//         githash = fs.readFileSync(revpath).toString().trim();
-//     }
-// } catch (e) {
-//     console.error("Error determining git hash")
-// }
-
-
 const versionJS = require.resolve('../js/version.js')
 let ping = fs.readFileSync(versionJS, 'utf-8');
 const lines = ping.split(/\r?\n/);
@@ -29,7 +12,6 @@ var fd = fs.openSync(versionJS, 'w');
 for (let line of lines) {
     if(!line) continue;
     if(line.startsWith("const _version")) {
-        //fs.writeSync(fd, `const _version = "${version} (${githash})"\n`, null, 'utf-8')
         fs.writeSync(fd, `const _version = "${version}"\n`, null, 'utf-8')
         foundVersionLine = true;
     } else {