trackster: Supports display of reference sequence in twobit format. Mapping of dbkey to twobit file is done in tool-data/twobit.loc. Reference track will automatically be shown when zoomed in if the twobit file exists for that dbkey. Also fixes a drawing issue with Reference/Read tracks.

2026-09-24 16:30:27 +08:00 · 2010-06-15 17:51:12 -04:00
parent c2335891ad
commit ce75edfa5f
4 changed files with 136 additions and 34 deletions
@@ -13,9 +13,10 @@ Problems
   need to support that, but need to make user defined build support better)
 """

-import math, re, logging, glob
-log = logging.getLogger(__name__)
+import math, re, logging, glob, pkg_resources
+pkg_resources.require( "bx-python" )

+from bx.seq.twobit import TwoBitFile
 from galaxy import model
 from galaxy.util.json import to_json_string, from_json_string
 from galaxy.web.base.controller import *
@@ -71,11 +72,9 @@ class DatasetSelectionGrid( grids.Grid ):
        DbKeyColumn( "Dbkey", key="dbkey", model_class=model.HistoryDatasetAssociation, visible=False )
    ]
    columns.append( 
-        grids.MulticolFilterColumn(  
-        "Search", 
-        cols_to_filter=[ columns[0], columns[1] ], 
+        grids.MulticolFilterColumn( "Search", cols_to_filter=[ columns[0], columns[1] ], 
        key="free-text-search", visible=False, filterable="standard" )
-                )
+    )
    
    def build_initial_query( self, trans, **kwargs ):
        return trans.sa_session.query( self.model_class ).join( model.History.table).join( model.Dataset.table )
@@ -96,6 +95,15 @@ class TracksController( BaseController, UsesVisualization ):
    """
    
    available_tracks = None
+    available_genomes = None
+    
+    def _init_references(self, trans):
+        avail_genomes = {}
+        for line in open( os.path.join( trans.app.config.tool_data_path, "twobit.loc" ) ):
+            if line.startswith("#"): continue
+            key, path = line.split()
+            avail_genomes[key] = path
+        self.available_genomes = avail_genomes
    
    @web.expose
    @web.require_login()
@@ -170,12 +178,16 @@ class TracksController( BaseController, UsesVisualization ):
            # No vis_id, so visualization is new. User is current user, dbkey must be given.
            vis_user = trans.user
            vis_dbkey = dbkey
-            
+        
        # Get chroms data.
        chroms = self._chroms( trans, vis_user, vis_dbkey )
+        
+        # Check for reference chrom
+        if self.available_genomes is None: self._init_references(trans)        
+        
        to_sort = [{ 'chrom': chrom, 'len': length } for chrom, length in chroms.iteritems()]
        to_sort.sort(lambda a,b: cmp( split_by_number(a['chrom']), split_by_number(b['chrom']) ))
-        return to_sort
+        return { 'reference': vis_dbkey in self.available_genomes, 'chrom_info': to_sort }

    def _chroms( self, trans, user, dbkey ):
        """
@@ -204,7 +216,24 @@ class TracksController( BaseController, UsesVisualization ):
            fields = line.split("\t")
            manifest[fields[0]] = int(fields[1])
        return manifest
+        
+    @web.json
+    def reference( self, trans, dbkey, chrom, low, high, **kwargs ):
+        if self.available_genomes is None: self._init_references(trans)

+        if dbkey not in self.available_genomes: 
+            return None
+        
+        try:
+            twobit = TwoBitFile( open(self.available_genomes[dbkey]) )
+        except IOError:
+            return None
+            
+        if chrom in twobit:
+            return twobit[chrom].get(int(low), int(high))        
+        
+        return None
+        
    @web.json
    def data( self, trans, dataset_id, chrom, low, high, **kwargs ):
        """
@@ -13,6 +13,7 @@ var DENSITY = 200,
    CACHED_TILES_LINE = 30,
    CACHED_DATA = 5,
    CONTEXT = $("<canvas></canvas>").get(0).getContext("2d"),
+    PX_PER_CHAR = CONTEXT.measureText("A").width,
    RIGHT_STRAND, LEFT_STRAND;
    
 var right_img = new Image();
@@ -206,7 +207,7 @@ $.extend( Track.prototype, {
        track.data_queue = {};
        track.tile_cache.clear();
        track.data_cache.clear();
-        track.content_div.css( "height", "30px" );
+        // track.content_div.css( "height", "30px" );
        if (!track.content_div.text()) {
            track.content_div.text(DATA_LOADING);
        }
@@ -252,6 +253,7 @@ $.extend( Track.prototype, {
 });

 var TiledTrack = function() {
+    this.left_offset = 200;
 };
 $.extend( TiledTrack.prototype, Track.prototype, {
    draw: function() {
@@ -333,6 +335,75 @@ $.extend( LabelTrack.prototype, Track.prototype, {
    }
 });

+var ReferenceTrack = function () {
+    this.track_type = "ReferenceTrack";
+    Track.call( this, null, $("#top-labeltrack") );
+    TiledTrack.call( this );
+    
+    this.hidden = true;
+    this.height_px = 12;
+    this.container_div.addClass( "reference-track" );
+    this.dummy_canvas = $("<canvas></canvas>").get(0).getContext("2d");
+    this.data_queue = {};
+    this.data_cache = new Cache(CACHED_DATA);
+    this.tile_cache = new Cache(CACHED_TILES_LINE);
+};
+$.extend( ReferenceTrack.prototype, TiledTrack.prototype, {
+    get_data: function(resolution, position) {
+        var track = this,
+            low = position * DENSITY * resolution,
+            high = ( position + 1 ) * DENSITY * resolution,
+            key = resolution + "_" + position;
+        
+        if (!track.data_queue[key]) {
+            track.data_queue[key] = true;
+            $.ajax({ 'url': reference_url, 'dataType': 'json', 'data': {  "chrom": this.view.chrom,
+                                    "low": low, "high": high, "dbkey": this.view.dbkey },
+                success: function (seq) {
+                    track.data_cache.set(key, seq);
+                    delete track.data_queue[key];
+                    track.draw();
+                }, error: function(r, t, e) {
+                    console.log(r, t, e);
+                }
+            });
+        }
+    },
+    draw_tile: function( resolution, tile_index, parent_element, w_scale ) {
+        var tile_low = tile_index * DENSITY * resolution,
+            tile_length = DENSITY * resolution,
+            canvas = $("<canvas class='tile'></canvas>"),
+            ctx = canvas.get(0).getContext("2d"),
+            key = resolution + "_" + tile_index;
+        
+        if (w_scale > PX_PER_CHAR) {
+            if (this.data_cache.get(key) === undefined) {
+                this.get_data( resolution, tile_index );
+                return;
+            }
+            
+            var seq = this.data_cache.get(key);
+            if (seq === null) { return; }
+            
+            canvas.get(0).width = Math.ceil( tile_length * w_scale + this.left_offset);
+            canvas.get(0).height = this.height_px;
+            
+            canvas.css( {
+                position: "absolute",
+                top: 0,
+                left: ( tile_low - this.view.low ) * w_scale + this.left_offset
+            });
+            
+            for (var c = 0, str_len = seq.length; c < str_len; c++) {
+                var c_start = Math.round(c * w_scale);
+                ctx.fillText(seq[c], c_start + this.left_offset, 10);
+            }
+            parent_element.append( canvas );
+            return canvas;
+        }
+    }
+});
+
 var LineTrack = function ( name, dataset_id, prefs ) {
    this.track_type = "LineTrack";
    Track.call( this, name, $("#viewport") );
@@ -400,14 +471,14 @@ $.extend( LineTrack.prototype, TiledTrack.prototype, {
            $.ajax({ 'url': data_url, 'dataType': 'json', 'data': {  "chrom": this.view.chrom, 
                                    "low": low, "high": high, "dataset_id": this.dataset_id,
                                    "resolution": this.view.resolution }, 
-            success: function (result) {
-                data = result.data;
-                track.data_cache.set(key, data);
-                delete track.data_queue[key];
-                track.draw();
-            }, error: function(r, t, e) {
-                console.log(r, t, e);
-            } 
+                success: function (result) {
+                    data = result.data;
+                    track.data_cache.set(key, data);
+                    delete track.data_queue[key];
+                    track.draw();
+                }, error: function(r, t, e) {
+                    console.log(r, t, e);
+                } 
            });
        }
    },
@@ -435,7 +506,7 @@ $.extend( LineTrack.prototype, TiledTrack.prototype, {
            left: ( tile_low - this.view.low ) * w_scale
        });
        
-        canvas.get(0).width = Math.ceil( tile_length * w_scale );
+        canvas.get(0).width = Math.ceil( tile_length * w_scale + this.left_offset);
        canvas.get(0).height = this.height_px;
        var ctx = canvas.get(0).getContext("2d"),
            in_path = false,
@@ -567,7 +638,6 @@ var FeatureTrack = function ( name, dataset_id, prefs ) {
    this.vertical_detail_px = 10;
    this.vertical_nodetail_px = 3;
    this.default_font = "9px Monaco, Lucida Console, monospace";
-    this.left_offset = 200;
    this.inc_slots = {};
    this.data_queue = {};
    this.s_e_by_tile = {};
@@ -718,10 +788,10 @@ $.extend( FeatureTrack.prototype, TiledTrack.prototype, {
        return highest_slot;
        
    },
-    rect_or_text: function( ctx, w_scale, px_per_char, tile_low, tile_high, feature_start, name, x, x_len, y_center ) {
+    rect_or_text: function( ctx, w_scale, tile_low, tile_high, feature_start, name, x, x_len, y_center ) {
        ctx.textAlign = "center";
        var gap = Math.round(w_scale / 2);
-        if ( (this.mode === "Pack" || this.mode === "Auto") && name !== undefined && w_scale > px_per_char) {
+        if ( (this.mode === "Pack" || this.mode === "Auto") && name !== undefined && w_scale > PX_PER_CHAR) {
            ctx.fillStyle = this.prefs.block_color;
            ctx.fillRect(x, y_center + 1, x_len, 9);
            ctx.fillStyle = "#eee";
@@ -790,8 +860,7 @@ $.extend( FeatureTrack.prototype, TiledTrack.prototype, {
        new_canvas.get(0).height = required_height;
        parent_element.parent().css("height", Math.max(this.height_px, required_height) + "px");
        // console.log(( tile_low - this.view.low ) * w_scale, tile_index, w_scale);
-        var ctx = new_canvas.get(0).getContext("2d"),
-            px_per_char = ctx.measureText("A").width;
+        var ctx = new_canvas.get(0).getContext("2d");
        ctx.fillStyle = block_color;
        ctx.font = this.default_font;
        ctx.textAlign = "right";
@@ -857,10 +926,10 @@ $.extend( FeatureTrack.prototype, TiledTrack.prototype, {
                            b2_end   = Math.ceil( Math.min(width, Math.max(0, (feature[5][1] - tile_low) * w_scale)) );
                        
                        if (feature[4][1] >= tile_low && feature[4][0] <= tile_high) {
-                            this.rect_or_text(ctx, w_scale, px_per_char, tile_low, tile_high, feature[4][0], feature[4][2], b1_start + left_offset, b1_end - b1_start, y_center);
+                            this.rect_or_text(ctx, w_scale, tile_low, tile_high, feature[4][0], feature[4][2], b1_start + left_offset, b1_end - b1_start, y_center);
                        }
                        if (feature[5][1] >= tile_low && feature[5][0] <= tile_high) {
-                            this.rect_or_text(ctx, w_scale, px_per_char, tile_low, tile_high, feature[5][0], feature[5][2], b2_start + left_offset, b2_end - b2_start, y_center);
+                            this.rect_or_text(ctx, w_scale, tile_low, tile_high, feature[5][0], feature[5][2], b2_start + left_offset, b2_end - b2_start, y_center);
                        }
                        if (b2_start > b1_end) {
                            ctx.fillStyle = "#999";
@@ -868,7 +937,7 @@ $.extend( FeatureTrack.prototype, TiledTrack.prototype, {
                        }
                    } else {
                        ctx.fillStyle = block_color;
-                        this.rect_or_text(ctx, w_scale, px_per_char, tile_low, tile_high, feature_start, feature_name, f_start + left_offset, f_end - f_start, y_center);
+                        this.rect_or_text(ctx, w_scale, tile_low, tile_high, feature_start, feature_name, f_start + left_offset, f_end - f_start, y_center);
                    }
                    if (mode !== "Dense" && !no_detail && feature_start > tile_low) {
                        // Draw label
@@ -30,7 +30,8 @@ ${h.css( "history", "autocomplete_tagging" )}

 <%def name="center_panel()">
 <div class="unified-panel-header" unselectable="on">
-    <div class="unified-panel-header-inner" id="title">
+    <div class="unified-panel-header-inner">
+        <div style="float:left;" id="title"></div>
        <a id="save-button" class="panel-header-button right-float" href="javascript:void(0);">Save</a>
        <a id="refresh-button" class="panel-header-button right-float" href="javascript:void(0);" onclick="view.update_options();return false;">Refresh</a>
    </div>
@@ -90,12 +91,12 @@ ${h.js( 'galaxy.base', 'galaxy.panels', "json2", "jquery", "jquery.event.drag",
 <script type="text/javascript">

    var data_url = "${h.url_for( action='data' )}";
+    var reference_url = "${h.url_for( action='reference' )}";
    var view;
    
    $(function() {
        
        %if config:
-            $("#title").text("${config.get('title') | h}");
            view = new View( "${config.get('chrom')}", "${config.get('title') | h}", "${config.get('vis_id')}", "${config.get('dbkey')}" );
            %for track in config.get('tracks'):
                view.add_track( 
@@ -106,7 +107,6 @@ ${h.js( 'galaxy.base', 'galaxy.panels', "json2", "jquery", "jquery.event.drag",
        %else:
            continue_fn = function() {
                view = new View( undefined, $("#new-title").val(), undefined, $("#new-dbkey").val() );
-                $("#title").text($("#new-title").val());
                init();
                hide_modal();
            };
@@ -133,6 +133,7 @@ ${h.js( 'galaxy.base', 'galaxy.panels', "json2", "jquery", "jquery.event.drag",
        
        // Execute this when everything is ready
        function init() {
+            $("#title").text(view.title + " (" + view.dbkey + ")");
            $("ul#sortable-ul").sortable({
                update: function(event, ui) {
                    for (var track_id in view.tracks) {
@@ -327,11 +328,14 @@ ${h.js( 'galaxy.base', 'galaxy.panels', "json2", "jquery", "jquery.event.drag",
                    data: { dbkey: view.dbkey },
                %endif
                dataType: "json",
-                success: function ( data ) {
-                    view.chrom_data = data;
+                success: function ( result ) {
+                    if (result['reference']) {
+                        view.add_label_track( new ReferenceTrack() );
+                    }
+                    view.chrom_data = result['chrom_info'];
                    var chrom_options = '<option value="">Select Chrom/Contig</option>';
-                    for (i in data) {
-                        var chrom = data[i]['chrom'];
+                    for (i in view.chrom_data) {
+                        var chrom = view.chrom_data[i]['chrom'];
                        chrom_options += '<option value="' + chrom + '">' + chrom + '</option>';
                    }
                    $("#chrom").html(chrom_options);