From 5962f0ab2e46b1facbb89f8fe1e3d2baf0541a4f Mon Sep 17 00:00:00 2001 From: Kanwei Li Date: Fri, 10 Dec 2010 14:59:43 -0500 Subject: [PATCH] trackster: Add bigWig display to trackster. Automatically converts wig to bigwig if needed (NOTE: datatypes_conf.xml.sample has been edited to add the new converter, you must update datatypes_conf.xml to use it). The converter requires that wigToBigWig be in the PATH, but no other tools are needed to view bigwig files as they are provided by bx_python. - Fix track preferences not being applied - Fix chroms not being selectable when a new track browser is created - Fix ReferenceTrack not working with filters - Fix visual analytics error when tool configuration has changed --- datatypes_conf.xml.sample | 1 + eggs.ini | 4 +- lib/galaxy/datatypes/binary.py | 2 + .../converters/wig_to_bigwig_converter.xml | 14 +++++ lib/galaxy/datatypes/interval.py | 2 +- .../visualization/tracks/data_providers.py | 60 ++++++++++++++++++- .../visualization/tracks/visual_analytics.py | 2 +- lib/galaxy/web/controllers/tracks.py | 24 +++++--- static/scripts/packed/trackster.js | 2 +- static/scripts/trackster.js | 54 ++++++++++------- templates/tracks/browser.mako | 4 +- 11 files changed, 130 insertions(+), 39 deletions(-) create mode 100644 lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml diff --git a/datatypes_conf.xml.sample b/datatypes_conf.xml.sample index 1536ccd041e..27214ada5ba 100644 --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -121,6 +121,7 @@ + diff --git a/eggs.ini b/eggs.ini index 6e1a5583fad..05225c80abe 100644 --- a/eggs.ini +++ b/eggs.ini @@ -12,7 +12,7 @@ repository = http://eggs.g2.bx.psu.edu/new no_auto = pbs_python DRMAA_python [eggs:platform] -bx_python = 0.5.0 +bx_python = 0.7.0 Cheetah = 2.2.2 ctypes = 1.0.2 DRMAA_python = 0.2 @@ -65,7 +65,7 @@ Whoosh = 0.3.18 psycopg2 = _8.4.2_static pysqlite = _3.6.17_static MySQL_python = _5.1.41_static -bx_python = _dev_f74aec067563 +bx_python = _14b6a6c95da6 GeneTrack = _dev_48da9e998f0caf01c5be731e926f4b0481f658f0 SQLAlchemy = _dev_r6498 pysam = _kanwei_90e03180969d diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py index 732ac88a798..7b043d9aa53 100644 --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -230,6 +230,8 @@ class BigWig(Binary): return dataset.peek except: return "Binary UCSC %s file (%s)" % ( self._name, data.nice_size( dataset.get_size() ) ) + def get_track_type( self ): + return "LineTrack", {"data_standalone": "bigwig"} class BigBed(BigWig): """BigBed support from UCSC.""" diff --git a/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml new file mode 100644 index 00000000000..0dcf7b51469 --- /dev/null +++ b/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml @@ -0,0 +1,14 @@ + \ No newline at end of file diff --git a/lib/galaxy/datatypes/interval.py b/lib/galaxy/datatypes/interval.py index f4070ef2e9c..778de245fff 100644 --- a/lib/galaxy/datatypes/interval.py +++ b/lib/galaxy/datatypes/interval.py @@ -1169,7 +1169,7 @@ class Wiggle( Tabular, _RemoteCallMixin ): resolution = max( resolution, 1 ) return resolution def get_track_type( self ): - return "LineTrack", {"data": "array_tree"} + return "LineTrack", {"data": "bigwig"} class CustomTrack ( Tabular ): """UCSC CustomTrack""" diff --git a/lib/galaxy/visualization/tracks/data_providers.py b/lib/galaxy/visualization/tracks/data_providers.py index f997ea95801..35e93b144a3 100644 --- a/lib/galaxy/visualization/tracks/data_providers.py +++ b/lib/galaxy/visualization/tracks/data_providers.py @@ -8,6 +8,7 @@ pkg_resources.require( "bx-python" ); pkg_resources.require( "pysam" ); pkg_reso from galaxy.datatypes.util.gff_util import * from bx.interval_index_file import Indexes from bx.arrays.array_tree import FileArrayTreeDict +from bx.bbi.bigwig_file import BigWigFile from galaxy.util.lrucache import LRUCache from galaxy.visualization.tracks.summary import * from galaxy.datatypes.tabular import Vcf @@ -16,6 +17,13 @@ from pysam import csamtools MAX_VALS = 5000 # only display first MAX_VALS features +# Return None instead of NaN to pass jQuery 1.4's strict JSON +def float_nan(n): + if n != n: # NaN != NaN + return None + else: + return float(n) + class TracksDataProvider( object ): """ Base class for tracks data providers. """ @@ -340,6 +348,50 @@ class ArrayTreeDataProvider( TracksDataProvider ): f.close() return results + +class BigWigDataProvider( TracksDataProvider ): + """ + BigWig data provider for the Galaxy track browser. + """ + + def get_data( self, chrom, start, end, **kwargs ): + # Bigwig has the possibility of it being a standalone bigwig file, in which case we use + # original_dataset, or coming from wig->bigwig conversion in which we use converted_dataset + if self.converted_dataset is not None: + f = open( self.converted_dataset.file_name ) + else: + f = open( self.original_dataset.file_name ) + bw = BigWigFile(file=f) + + if 'stats' in kwargs: + all_dat = bw.query(chrom, 0, 2147483647, 1) + f.close() + if all_dat is None: + return None + + all_dat = all_dat[0] # only 1 summary + return { 'max': float( all_dat['max'] ), \ + 'min': float( all_dat['min'] ), \ + 'total_frequency': float( all_dat['coverage'] ) } + + + start = int(start) + end = int(end) + num_points = 2000 + if (end - start) < num_points: + num_points = end - start + + data = bw.query(chrom, start, end, num_points) + f.close() + + pos = start + step_size = (end - start) / num_points + result = [] + for dat_dict in data: + result.append( (pos, float_nan(dat_dict['mean']) ) ) + pos += step_size + + return result class IntervalIndexDataProvider( TracksDataProvider ): """ @@ -448,7 +500,8 @@ dataset_type_name_to_data_provider = { "array_tree": ArrayTreeDataProvider, "interval_index": { "vcf": VcfDataProvider, "default" : IntervalIndexDataProvider }, "bai": BamDataProvider, - "summary_tree": SummaryTreeDataProvider + "summary_tree": SummaryTreeDataProvider, + "bigwig": BigWigDataProvider } dataset_type_to_data_provider = { @@ -477,7 +530,10 @@ def get_data_provider( name=None, original_dataset=None ): # Get data provider mapping and data provider for 'data'. If # provider available, use it; otherwise use generic provider. _ , data_provider_mapping = original_dataset.datatype.get_track_type() - data_provider_name = data_provider_mapping[ 'data' ] + if 'data_standalone' in data_provider_mapping: + data_provider_name = data_provider_mapping[ 'data_standalone' ] + else: + data_provider_name = data_provider_mapping[ 'data' ] if data_provider_name: data_provider = get_data_provider( name=data_provider_name, original_dataset=original_dataset ) else: diff --git a/lib/galaxy/visualization/tracks/visual_analytics.py b/lib/galaxy/visualization/tracks/visual_analytics.py index f20c90d874e..bb09804ba00 100644 --- a/lib/galaxy/visualization/tracks/visual_analytics.py +++ b/lib/galaxy/visualization/tracks/visual_analytics.py @@ -26,7 +26,7 @@ def get_tool_def( trans, hda ): # Get list of tool parameters that can be interactively modified. tool_params = [] tool_param_values = dict( [ ( p.name, p.value ) for p in job.parameters ] ) - tool_param_values = tool.params_from_strings( tool_param_values, trans.app ) + tool_param_values = tool.params_from_strings( tool_param_values, trans.app, ignore_errors=True ) for name, input in tool.inputs.items(): if type( input ) == IntegerToolParameter: tool_params.append( { 'name' : name, 'label': input.label, 'type': 'int', \ diff --git a/lib/galaxy/web/controllers/tracks.py b/lib/galaxy/web/controllers/tracks.py index 75571ae61e8..be9a5cdad23 100644 --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -120,7 +120,6 @@ class TracksController( BaseController, UsesVisualization, UsesHistoryDatasetAss @web.require_login() def index( self, trans, **kwargs ): config = {} - return trans.fill_template( "tracks/browser.mako", config=config, add_dataset=kwargs.get("dataset_id", None), \ default_dbkey=kwargs.get("default_dbkey", None) ) @@ -267,7 +266,7 @@ class TracksController( BaseController, UsesVisualization, UsesHistoryDatasetAss return msg # Get converted datasets. - data_sources, message = self._get_converted_datasets( trans, dataset ) + data_sources, message = self._get_datasource_info( trans, dataset ) if not data_sources: return message @@ -286,9 +285,14 @@ class TracksController( BaseController, UsesVisualization, UsesHistoryDatasetAss return { 'dataset_type': data_sources['index'], 'data': frequencies, 'max': max_v, 'avg': avg_v, 'delta': delta } # Get data provider. - tracks_dataset_type = data_sources['data'] - data_provider_class = get_data_provider( name=tracks_dataset_type, original_dataset=dataset ) - data_provider = data_provider_class( dataset.get_converted_dataset(trans, tracks_dataset_type), dataset ) + if "data_standalone" in data_sources: + tracks_dataset_type = data_sources['data_standalone'] + data_provider_class = get_data_provider( name=tracks_dataset_type, original_dataset=dataset ) + data_provider = data_provider_class( original_dataset=dataset ) + else: + tracks_dataset_type = data_sources['data'] + data_provider_class = get_data_provider( name=tracks_dataset_type, original_dataset=dataset ) + data_provider = data_provider_class( dataset.get_converted_dataset(trans, tracks_dataset_type), dataset ) # Get and return data from data_provider. data = data_provider.get_data( chrom, low, high, **kwargs ) @@ -502,13 +506,17 @@ class TracksController( BaseController, UsesVisualization, UsesHistoryDatasetAss return messages.PENDING return None - def _get_converted_datasets( self, trans, dataset ): + def _get_datasource_info( self, trans, dataset ): """ - Returns (a) converted datasets for a dataset and (b) dictionary of + Returns (a) datasource info for a dataset and (b) dictionary of any messages based on or derived from the conversion. 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").appendTo(d.header_div);var g=d.display_modes[0];d.mode=g;d.mode_div.text(g);var e=function(i){d.mode_div.text(i);d.mode=i;d.tile_cache.clear();d.draw()};var a={};for(var h=0,k=d.display_modes.length;h0){f["Show filters"]=function(){var i;if(!d.filtering_div.is(":visible")){i="Hide filters";d.filters_visible=true}else{i="Show filters";d.filters_visible=false}d.filtering_div.toggle()}}if(d.tool){f["Toggle Tool Controls"]=function(){var i;if(!d.dynamic_tool_div.is(":visible")){i="Hide dynamic tool"}else{i="Show dynamic tool"}d.dynamic_tool_div.toggle()}}f.Remove=function(){o.remove_track(d);if(o.num_tracks===0){$("#no-tracks").show()}};d.popup_menu=make_popupmenu(d.name_div,f)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(a){var k=this.view.low,g=this.view.high,h=g-k,f=this.view.resolution;var n=$("
"),o=this.content_div.width()/h;this.content_div.append(n);this.max_height=0;var b=Math.floor(k/f/DENSITY);var j={};while((b*DENSITY*f)1){c.content_div.children(":first").remove()}for(var p=0;p=c.view.low){var k=c.draw_tile(d,b,i,j);if(k){if(!c.initial_canvas&&!window.G_vmlCanvasManager){c.initial_canvas=$(k).clone();var n=k.get(0).getContext("2d");var l=c.initial_canvas.get(0).getContext("2d");var m=n.getImageData(0,0,n.canvas.width,n.canvas.height);l.putImageData(m,0,0);c.set_overview()}c.tile_cache.set(h,k);c.show_tile(k,i)}}delete f[a]},50);f[a]=true},show_tile:function(a,c){var b=this;c.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var a={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name,};$.extend(a,this.tool.get_param_values_dict());var b=this;$.getJSON(run_tool_url,a,function(e){var c=a.tool_id+", region=["+a.chrom+":"+a.low+"-"+a.high+"], parameters=["+b.tool.get_param_values().join(", ")+"]";var g=e,d={LineTrack:LineTrack,FeatureTrack:FeatureTrack,ReadTrack:ReadTrack},f=new d[e.track_type](c,view,e.dataset_id,e.prefs,e.filters,e.tool,b);view.add_track(f)})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("
");while(a"+commatize(a)+"
").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.data_queue={};this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,j=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var n=e.get(0).getContext("2d");if(o>PX_PER_CHAR){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;e.css({position:"absolute",top:0,left:(g-this.view.low)*o-this.left_offset});for(var h=0,l=m.length;h").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("
").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",top:a.height_px+12+"px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*o,a=DENSITY*o,w=o+"_"+r;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(w)===undefined){this.get_data(o,r);return}var v=this.data_cache.get(w);if(!v){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;n.beginPath();n.fillStyle=this.prefs.color;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;pg){h=g}}if(l==="Histogram"){h=Math.round(d-(h-k)/m*d);n.fillRect(u,h,f,d-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,d)}n.fill()}else{n.stroke()}c.append(b);return b},gen_options:function(m){var a=$("
").addClass("form-row");var e="track_"+m+"_color",b=$("