galaxy-dev October 2009

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172 discussions

[hg] galaxy 2799: Trackster: only attempt dataset conversion onc...
by Nate Coraor 02 Oct '09

02 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/62b897ca35ca changeset: 2799:62b897ca35ca user: Kanwei Li <kanwei(a)gmail.com> date: Tue Sep 29 21:50:44 2009 -0400 description: Trackster: only attempt dataset conversion once, UI/parsing improvements 8 file(s) affected in this change: lib/galaxy/datatypes/converters/bed_to_interval_index_converter.py lib/galaxy/visualization/tracks/data/array_tree.py lib/galaxy/web/controllers/tracks.py static/scripts/packed/trackster.js static/scripts/trackster.js static/trackster.css templates/dataset/edit_attributes.mako templates/tracks/new_browser.mako diffs (425 lines): diff -r e7b9d15e8e93 -r 62b897ca35ca lib/galaxy/datatypes/converters/bed_to_interval_index_converter.py --- a/lib/galaxy/datatypes/converters/bed_to_interval_index_converter.py Tue Sep 29 17:57:45 2009 -0400 +++ b/lib/galaxy/datatypes/converters/bed_to_interval_index_converter.py Tue Sep 29 21:50:44 2009 -0400 @@ -16,7 +16,7 @@ for line in open(input_fname, "r"): feature = line.split() - if feature[0] == "track": + if not feature or feature[0] == "track" or feature[0] == "#": offset += len(line) continue chrom = feature[0] diff -r e7b9d15e8e93 -r 62b897ca35ca lib/galaxy/visualization/tracks/data/array_tree.py --- a/lib/galaxy/visualization/tracks/data/array_tree.py Tue Sep 29 17:57:45 2009 -0400 +++ b/lib/galaxy/visualization/tracks/data/array_tree.py Tue Sep 29 21:50:44 2009 -0400 @@ -24,7 +24,7 @@ try: chrom_array_tree = d[chrom] except KeyError: - return None + return "no data" root_summary = chrom_array_tree.get_summary( 0, chrom_array_tree.levels ) return { 'max': float( max(root_summary.maxs) ), 'min': float( min(root_summary.mins) ) } @@ -33,9 +33,8 @@ start = int( start ) end = int( end ) level = int( ceil( log( end - start, BLOCK_SIZE ) ) ) - 1 - print "!!!!", start, end, level + # Open the file - print self.dataset.file_name d = FileArrayTreeDict( open( self.dataset.file_name ) ) # Get the right chromosome try: diff -r e7b9d15e8e93 -r 62b897ca35ca lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py Tue Sep 29 17:57:45 2009 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Tue Sep 29 21:50:44 2009 -0400 @@ -9,8 +9,6 @@ Problems -------- - - Only line tracks supported - - Resolutions are a bit wonky - Must have a LEN file, not currently able to infer from data (not sure we need to support that, but need to make user defined build support better) """ @@ -31,7 +29,8 @@ PENDING = "pending", NO_DATA = "no data", NO_CHROMOSOME = "no chromosome", - DATA = "data" + DATA = "data", + ERROR = "error" ) # Dataset type required for each track type. This needs to be more flexible, @@ -57,11 +56,11 @@ Controller for track browser interface. Handles building a new browser from datasets in the current history, and display of the resulting browser. """ - + @web.expose def index( self, trans ): return trans.fill_template( "tracks/index.mako" ) - + @web.expose def new_browser( self, trans, dbkey=None, dataset_ids=None, browse=None ): """ @@ -72,13 +71,16 @@ # If the user clicked the submit button explicitly, try to build the browser if browse and dataset_ids: if not isinstance( dataset_ids, list ): - dataset_ids = [ dataset_ids ] + dataset_ids = [ dataset_ids ] dataset_ids = ",".join( map( str, dataset_ids ) ) trans.response.send_redirect( web.url_for( controller='tracks', action='browser', chrom="", dataset_ids=dataset_ids ) ) else: # Determine the set of all dbkeys that are used in the current history dbkeys = [ d.metadata.dbkey for d in trans.get_history().datasets if not d.deleted ] dbkey_set = set( dbkeys ) + if not dbkey_set: + return trans.show_error_message( "Current history has no valid datasets to visualize." ) + # If a dbkey argument was not provided, or is no longer valid, default # to the first one if dbkey is None or dbkey not in dbkey_set: @@ -88,7 +90,7 @@ datasets = {} for dataset in session.query( model.HistoryDatasetAssociation ).filter_by( deleted=False, history_id=trans.history.id ): if dataset.metadata.dbkey == dbkey and dataset.extension in browsable_types: - datasets[dataset.id] = dataset.name + datasets[dataset.id] = (dataset.extension, dataset.name) # Render the template return trans.fill_template( "tracks/new_browser.mako", dbkey=dbkey, dbkey_set=dbkey_set, datasets=datasets ) @@ -110,13 +112,13 @@ chrom_lengths = self._chroms( trans, dbkey ) if chrom_lengths is None: error( "No chromosome lengths file found for '%s'" % dataset.name ) - return trans.fill_template( 'tracks/browser.mako', + return trans.fill_template( 'tracks/browser.mako', dataset_ids=dataset_ids, tracks=tracks, chrom=chrom, dbkey=dbkey, LEN=chrom_lengths.get(chrom, 0) ) - + @web.json def chroms(self, trans, dbkey=None ): """ @@ -127,15 +129,15 @@ return int(s) else: return s - + def split_by_number(s): return [ check_int(c) for c in re.split('([0-9]+)', s) ] - + chroms = self._chroms( trans, dbkey ) 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 - + def _chroms( self, trans, dbkey ): """ Called by the browser to get a list of valid chromosomes and lengths @@ -155,8 +157,8 @@ fields = line.split("\t") manifest[fields[0]] = int(fields[1]) return manifest - - @web.json + + @web.json def data( self, trans, dataset_id, track_type, chrom, low, high, stats=False ): """ Called by the browser to request a block of data @@ -168,34 +170,32 @@ return messages.NO_DATA # Dataset is in error state, can't display if dataset.state == trans.app.model.Job.states.ERROR: - return messages.NO_DATA + return messages.ERROR # Dataset is still being generated if dataset.state != trans.app.model.Job.states.OK: return messages.PENDING # Determine what to return based on the type of track being drawn. - converted_dataset_type = track_type_to_dataset_type[track_type] + converted_dataset_type = track_type_to_dataset_type[track_type] converted_dataset = self.__dataset_as_type( trans, dataset, converted_dataset_type ) # If at this point we still don't have an `array_tree_dataset`, there # is no way we can display this data as an array tree - if converted_dataset is None: - return messages.NO_DATA + if not converted_dataset: + return messages.ERROR # Need to check states again for the converted version if converted_dataset.state == model.Dataset.states.ERROR: - return messages.NO_DATA + return messages.ERROR if converted_dataset.state != model.Dataset.states.OK: return messages.PENDING # We have a dataset in the right format that is ready to use, wrap in # a data provider that knows how to access it data_provider = dataset_type_to_data_provider[ converted_dataset_type ]( converted_dataset, dataset ) - + # Return stats if we need them if stats: return data_provider.get_stats( chrom ) - + # Get the requested chunk of data - data = data_provider.get_data( chrom, low, high ) - # Pack into a dictionary and return - return data - + return data_provider.get_data( chrom, low, high ) + def __dataset_as_type( self, trans, dataset, type ): """ Given a dataset, try to find a way to adapt it to a different type. If the @@ -211,12 +211,15 @@ log.debug( "Conversion from '%s' to '%s' not possible", dataset.extension, type ) return None # See if converted dataset already exists - converted_datasets = dataset.get_converted_files_by_type( type ) + converted_datasets = [c for c in dataset.get_converted_files_by_type( type ) if c != None] if converted_datasets: for d in converted_datasets: - if d and d.state != 'error': + if d.state != 'error': return d - # Conversion is possible but doesn't exist yet, run converter here + else: + return None + + # Conversion is possible but hasn't been done yet, run converter here # FIXME: this is largely duplicated from DefaultToolAction assoc = model.ImplicitlyConvertedDatasetAssociation( parent = dataset, file_type = type, metadata_safe = False ) new_dataset = dataset.datatype.convert_dataset( trans, dataset, type, return_output = True, visible = False ).values()[0] diff -r e7b9d15e8e93 -r 62b897ca35ca static/scripts/packed/trackster.js --- a/static/scripts/packed/trackster.js Tue Sep 29 17:57:45 2009 -0400 +++ b/static/scripts/packed/trackster.js Tue Sep 29 21:50:44 2009 -0400 @@ -1,1 +1,1 @@ -var DENSITY=1000;var DataCache=function(b,a){this.type=b;this.track=a;this.cache=Object()};$.extend(DataCache.prototype,{get:function(d,b){var c=this.cache;if(!(c[d]&&c[d][b])){if(!c[d]){c[d]=Object()}var a=b*DENSITY*d;var e=(b+1)*DENSITY*d;c[d][b]={state:"loading"};$.getJSON(data_url,{track_type:this.track.track_type,chrom:this.track.view.chrom,low:a,high:e,dataset_id:this.track.dataset_id},function(f){if(f=="pending"){setTimeout(fetcher,5000)}else{c[d][b]={state:"loaded",values:f}}$(document).trigger("redraw")})}return c[d][b]}});var View=function(a,b){this.chrom=a;this.tracks=[];this.max_low=0;this.max_high=b;this.low=this.max_low;this.high=this.max_high;this.length=this.max_high-this.max_low};$.extend(View.prototype,{add_track:function(a){a.view=this;this.tracks.push(a);if(a.init){a.init()}},redraw:function(){$("#overview-box").css({left:(this.low/this.length)*$("#overview-viewport").width(),width:Math.max(4,((this.high-this.low)/this.length)*$("#overview-viewport").widt h())}).show();$("#low").text(this.low);$("#high").text(this.high);for(var a in this.tracks){this.tracks[a].draw()}$("#bottom-spacer").remove();$("#viewport").append('<div id="bottom-spacer" style="height: 200px;"></div>')},move:function(b,a){this.low=Math.max(this.max_low,Math.floor(b));this.high=Math.min(this.length,Math.ceil(a))},zoom_in:function(d,b){if(this.max_high==0){return}var c=this.high-this.low;var e=c/d/2;if(b==undefined){var a=(this.low+this.high)/2}else{var a=this.low+c*b/$(document).width()}this.low=Math.floor(a-e);this.high=Math.ceil(a+e);if(this.low<this.max_low){this.low=this.max_low;this.high=c/d}else{if(this.high>this.max_high){this.high=this.max_high;this.low=this.max_high-c/d}}if(this.high-this.low<1){this.high=this.low+1}},zoom_out:function(c){if(this.max_high==0){return}var a=(this.low+this.high)/2;var b=this.high-this.low;var d=b*c/2;this.low=Math.floor(Math.max(0,a-d));this.high=Math.ceil(Math.min(this.length,a+d))},left:function(b){var a=this.high- this.low;var c=Math.floor(a/b);if(this.low-c<0){this.low=0;this.high=this.low+a}else{this.low-=c;this.high-=c}},right:function(b){var a=this.high-this.low;var c=Math.floor(a/b);if(this.high+c>this.length){this.high=this.length;this.low=this.high-a}else{this.low+=c;this.high+=c}}});var Track=function(a,b){this.name=a;this.parent_element=b;this.make_container()};$.extend(Track.prototype,{make_container:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div class='track'></div>").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)}});var TiledTrack=function(){this.last_resolution=null;this.last_w_scale=null;this.tile_cache={}};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var k=this.view.low,c=this.view.high,e=c-k;var b=Math.pow(10,Math.ceil(Math.log(e/DENSITY)/Math.log(10)));b=Math.max(b,1);b=Math.min(b,100000);var o=$("< div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(o);var m=this.content_div.width(),d=this.content_div.height(),p=m/e,l={},n={};if(this.last_resolution==b&&this.last_w_scale==p){l=this.tile_cache}var g;var a=Math.floor(k/b/DENSITY);var i=0;while((a*1000*b)<c){if(a in l){g=l[a];var f=a*DENSITY*b;g.css({left:(f-this.view.low)*p});o.append(g)}else{g=this.draw_tile(b,a,o,p,d)}if(g){n[a]=g;i=Math.max(i,g.height())}a+=1}o.css("height",i);this.last_resolution=b;this.last_w_scale=p;this.tile_cache=n}});var LineTrack=function(c,b,a){Track.call(this,c,$("#viewport"));this.track_type="line";this.height_px=(a?a:100);this.container_div.addClass("line-track");this.dataset_id=b;this.cache=new DataCache("",this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{make_container:function(){Track.prototype.make_container.call(this);this.content_div.css("height",this.height_px)},init:function(){track=this;$.getJSON(data_url,{stats:tru e,track_type:track.track_type,chrom:this.view.chrom,low:null,high:null,dataset_id:this.dataset_id},function(a){if(a){track.min_value=a.min;track.max_value=a.max;track.vertical_range=track.max_value-track.min_value;track.view.redraw()}})},draw_tile:function(d,a,o,s,p){if(!this.vertical_range){return}var k=a*DENSITY*d,r=(a+1)*DENSITY*d,c=DENSITY*d;var n=this.cache.get(d,a);var h;if(n.state=="loading"){h=$("<div class='loading tile'></div>")}else{h=$("<canvas class='tile'></canvas>")}h.css({position:"absolute",top:0,left:(k-this.view.low)*s,});o.append(h);if(n.state=="loading"){e=false;return null}var b=h;b.get(0).width=Math.ceil(c*s);b.get(0).height=this.height_px;var q=b.get(0).getContext("2d");var e=false;q.beginPath();var g=n.values;if(!g){return}for(var f=0;f<g.length-1;f++){var m=g[f][0]-k;var l=g[f][1];if(isNaN(l)){e=false}else{m=m*s;y_above_min=l-this.min_value;l=y_above_min/this.vertical_range*this.height_px;if(e){q.lineTo(m,l)}else{q.moveTo(m,l);e=true}}}q.stroke();re turn h}});var LabelTrack=function(a){Track.call(this,null,a);this.container_div.addClass("label-track")};$.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=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+a+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var itemHeight=13,itemPad=3,thinHeight=7,thinOffset=3;var FeatureTrack=function(b,a){Track.call(this,b,$("#viewport"));this.track_type="feature";this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots=new Object();this.show_labels_scale=0.01;this.showing_labels=false};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{calc_slots:function(d){end_ary=new Array();var c=this.container_div.wid th()/(this.view.high-this.view.low);if(d){this.zi_slots=new Object()}var b=$("<canvas></canvas>").get(0).getContext("2d");for(var a in this.values){feature=this.values[a];f_start=Math.floor(Math.max(this.view.max_low,(feature.start-this.view.max_low)*c));if(d){f_start-=b.measureText(feature.name).width}f_end=Math.ceil(Math.min(this.view.max_high,(feature.end-this.view.max_low)*c));j=0;while(true){if(end_ary[j]==undefined||end_ary[j]<f_start){end_ary[j]=f_end;if(d){this.zi_slots[feature.name]=j}else{this.zo_slots[feature.name]=j}break}j++}}},init:function(){var a=this;$.getJSON(data_url,{track_type:a.track_type,low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){a.values=b;a.calc_slots();a.slots=a.zo_slots;a.draw()})},draw_tile:function(q,t,e,g,f){if(!this.values){return null}if(g>this.show_labels_scale&&!this.showing_labels){this.showing_labels=true;if(!this.zi_slots){this.calc_slots(true)}this.slots=this.zi_slots}else{if(g<=this.s how_labels_scale&&this.showing_labels){this.showing_labels=false;this.slots=this.zo_slots}}var u=t*DENSITY*q,c=(t+1)*DENSITY*q,b=DENSITY*q;var k=this.view,m=k.high-k.low,o=Math.ceil(b*g),h=new Array(),n=200,l=$("<canvas class='tile'></canvas>");l.css({position:"absolute",top:0,left:(u-this.view.low)*g,});l.get(0).width=o;l.get(0).height=n;var p=l.get(0).getContext("2d");var r=0;for(var s in this.values){feature=this.values[s];if(feature.start<=c&&feature.end>=u){f_start=Math.floor(Math.max(0,(feature.start-u)*g));f_end=Math.ceil(Math.min(o,(feature.end-u)*g));p.fillStyle="#000";p.fillRect(f_start,this.slots[feature.name]*10+5,f_end-f_start,1);if(this.showing_labels&&p.fillText){p.font="10px monospace";p.textAlign="right";p.fillText(feature.name,f_start,this.slots[feature.name]*10+8)}if(feature.exon_start&&feature.exon_end){var d=Math.floor(Math.max(0,(feature.exon_start-u)*g));var w=Math.ceil(Math.min(o,(feature.exon_end-u)*g))}for(var s in feature.blocks){block=feature.bloc ks[s];block_start=Math.floor(Math.max(0,(block[0]-u)*g));block_end=Math.ceil(Math.min(o,(block[1]-u)*g));var a=3,v=4;if(d&&block_start>=d&&block_end<=w){a=5,v=3}p.fillRect(d,this.slots[feature.name]*10+v,block_end-block_start,a)}r++}}e.append(l);return l},}); \ No newline at end of file +var DENSITY=1000;var DataCache=function(b,a){this.type=b;this.track=a;this.cache=Object()};$.extend(DataCache.prototype,{get:function(d,b){var c=this.cache;if(!(c[d]&&c[d][b])){if(!c[d]){c[d]=Object()}var a=b*DENSITY*d;var e=(b+1)*DENSITY*d;c[d][b]={state:"loading"};$.getJSON(data_url,{track_type:this.track.track_type,chrom:this.track.view.chrom,low:a,high:e,dataset_id:this.track.dataset_id},function(f){if(f=="pending"){setTimeout(fetcher,5000)}else{c[d][b]={state:"loaded",values:f}}$(document).trigger("redraw")})}return c[d][b]}});var View=function(a,b){this.chrom=a;this.tracks=[];this.max_low=0;this.max_high=b;this.low=this.max_low;this.high=this.max_high;this.length=this.max_high-this.max_low};$.extend(View.prototype,{add_track:function(a){a.view=this;this.tracks.push(a);if(a.init){a.init()}},redraw:function(){$("#overview-box").css({left:(this.low/this.length)*$("#overview-viewport").width(),width:Math.max(4,((this.high-this.low)/this.length)*$("#overview-viewport").widt h())}).show();$("#low").text(this.low);$("#high").text(this.high);for(var a in this.tracks){this.tracks[a].draw()}$("#bottom-spacer").remove();$("#viewport").append('<div id="bottom-spacer" style="height: 200px;"></div>')},move:function(b,a){this.low=Math.max(this.max_low,Math.floor(b));this.high=Math.min(this.length,Math.ceil(a))},zoom_in:function(d,b){if(this.max_high==0){return}var c=this.high-this.low;var e=c/d/2;if(b==undefined){var a=(this.low+this.high)/2}else{var a=this.low+c*b/$(document).width()}this.low=Math.floor(a-e);this.high=Math.ceil(a+e);if(this.low<this.max_low){this.low=this.max_low;this.high=c/d}else{if(this.high>this.max_high){this.high=this.max_high;this.low=this.max_high-c/d}}if(this.high-this.low<1){this.high=this.low+1}},zoom_out:function(c){if(this.max_high==0){return}var a=(this.low+this.high)/2;var b=this.high-this.low;var d=b*c/2;this.low=Math.floor(Math.max(0,a-d));this.high=Math.ceil(Math.min(this.length,a+d))},left:function(b){var a=this.high- this.low;var c=Math.floor(a/b);if(this.low-c<0){this.low=0;this.high=this.low+a}else{this.low-=c;this.high-=c}},right:function(b){var a=this.high-this.low;var c=Math.floor(a/b);if(this.high+c>this.length){this.high=this.length;this.low=this.high-a}else{this.low+=c;this.high+=c}}});var Track=function(a,b){this.name=a;this.parent_element=b;this.make_container()};$.extend(Track.prototype,{make_container:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div class='track'></div>").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)}});var TiledTrack=function(){this.last_resolution=null;this.last_w_scale=null;this.tile_cache={}};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var i=this.view.low,c=this.view.high,e=c-i;var b=Math.pow(10,Math.ceil(Math.log(e/DENSITY)/Math.log(10)));b=Math.max(b,1);b=Math.min(b,100000);var n=$("< div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(n);var l=this.content_div.width(),d=this.content_div.height(),o=l/e,k={},m={};if(this.last_resolution==b&&this.last_w_scale==o){k=this.tile_cache}var g;var a=Math.floor(i/b/DENSITY);while((a*1000*b)<c){if(a in k){g=k[a];var f=a*DENSITY*b;g.css({left:(f-this.view.low)*o});n.append(g)}else{g=this.draw_tile(b,a,n,o,d)}if(g){m[a]=g}a+=1}this.last_resolution=b;this.last_w_scale=o;this.tile_cache=m}});var LabelTrack=function(a){Track.call(this,null,a);this.container_div.addClass("label-track")};$.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=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+a+"</div>").css({position:"absolute",left:f-1 }));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,b,a){Track.call(this,c,$("#viewport"));this.track_type="line";this.height_px=(a?a:100);this.container_div.addClass("line-track");this.content_div.css("height",this.height_px+"px");this.dataset_id=b;this.cache=new DataCache("",this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;$.getJSON(data_url,{stats:true,track_type:a.track_type,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(b){if(b){if(b=="error"){a.content_div.addClass("error").text("There was an error in indexing this dataset.")}else{if(b=="no data"){a.content_div.addClass("nodata").text("No data for this chrom/contig.")}else{a.min_value=b.min;a.max_value=b.max;a.vertical_range=a.max_value-a.min_value;a.view.redraw()}}}})},draw_tile:function(d,a,o,s,p){if(!this.vertical_range){return}var k=a*DENSITY*d,r=(a+1)*DENSITY*d,c=DENSITY*d;var n=this.cache.get(d,a) ;var h;if(n.state=="loading"){h=$("<div class='loading tile'></div>")}else{h=$("<canvas class='tile'></canvas>")}h.css({position:"absolute",top:0,left:(k-this.view.low)*s,});o.append(h);if(n.state=="loading"){e=false;return null}var b=h;b.get(0).width=Math.ceil(c*s);b.get(0).height=this.height_px;var q=b.get(0).getContext("2d");var e=false;q.beginPath();var g=n.values;if(!g){return}for(var f=0;f<g.length-1;f++){var m=g[f][0]-k;var l=g[f][1];if(isNaN(l)){e=false}else{m=m*s;y_above_min=l-this.min_value;l=y_above_min/this.vertical_range*this.height_px;if(e){q.lineTo(m,l)}else{q.moveTo(m,l);e=true}}}q.stroke();return h}});var FeatureTrack=function(c,b,a){Track.call(this,c,$("#viewport"));this.track_type="feature";this.height_px=(a?a:100);this.container_div.addClass("feature-track");this.content_div.css("height",this.height_px+"px");this.dataset_id=b;this.zo_slots={};this.show_labels_scale=0.01;this.showing_labels=false};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{calc_ slots:function(e){var a=new Array();var d=this.container_div.width()/(this.view.high-this.view.low);if(e){this.zi_slots=new Object()}var c=$("<canvas></canvas>").get(0).getContext("2d");for(var b in this.values){feature=this.values[b];f_start=Math.floor(Math.max(this.view.max_low,(feature.start-this.view.max_low)*d));if(e){f_start-=c.measureText(feature.name).width}f_end=Math.ceil(Math.min(this.view.max_high,(feature.end-this.view.max_low)*d));j=0;while(true){if(a[j]==undefined||a[j]<f_start){a[j]=f_end;if(e){this.zi_slots[feature.name]=j}else{this.zo_slots[feature.name]=j}break}j++}}},init:function(){var a=this;$.getJSON(data_url,{track_type:a.track_type,low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){a.values=b;a.calc_slots();a.slots=a.zo_slots;a.draw()})},draw_tile:function(q,t,e,g,f){if(!this.values){return null}if(g>this.show_labels_scale&&!this.showing_labels){this.showing_labels=true;if(!this.zi_slots){this.calc_slots(tr ue)}this.slots=this.zi_slots}else{if(g<=this.show_labels_scale&&this.showing_labels){this.showing_labels=false;this.slots=this.zo_slots}}var u=t*DENSITY*q,c=(t+1)*DENSITY*q,b=DENSITY*q;var k=this.view,m=k.high-k.low,o=Math.ceil(b*g),h=new Array(),n=200,l=$("<canvas class='tile'></canvas>");l.css({position:"absolute",top:0,left:(u-this.view.low)*g,});l.get(0).width=o;l.get(0).height=n;var p=l.get(0).getContext("2d");var r=0;for(var s in this.values){feature=this.values[s];if(feature.start<=c&&feature.end>=u){f_start=Math.floor(Math.max(0,(feature.start-u)*g));f_end=Math.ceil(Math.min(o,(feature.end-u)*g));p.fillStyle="#000";p.fillRect(f_start,this.slots[feature.name]*10+5,f_end-f_start,1);if(this.showing_labels&&p.fillText){p.font="10px monospace";p.textAlign="right";p.fillText(feature.name,f_start,this.slots[feature.name]*10+8)}if(feature.exon_start&&feature.exon_end){var d=Math.floor(Math.max(0,(feature.exon_start-u)*g));var w=Math.ceil(Math.min(o,(feature.exon_end-u)*g))}f or(var s in feature.blocks){block=feature.blocks[s];block_start=Math.floor(Math.max(0,(block[0]-u)*g));block_end=Math.ceil(Math.min(o,(block[1]-u)*g));var a=3,v=4;if(d&&block_start>=d&&block_end<=w){a=5,v=3}p.fillRect(d,this.slots[feature.name]*10+v,block_end-block_start,a)}r++}}e.append(l);return l},}); \ No newline at end of file diff -r e7b9d15e8e93 -r 62b897ca35ca static/scripts/trackster.js --- a/static/scripts/trackster.js Tue Sep 29 17:57:45 2009 -0400 +++ b/static/scripts/trackster.js Tue Sep 29 21:50:44 2009 -0400 @@ -172,7 +172,6 @@ var tile_element; // Index of first tile that overlaps visible region var tile_index = Math.floor( low / resolution / DENSITY ); - var max_height = 0; while ( ( tile_index * 1000 * resolution ) < high ) { // Check in cache if ( tile_index in old_tiles ) { @@ -190,16 +189,38 @@ if ( tile_element ) { // console.log( typeof(tile_element) ); new_tiles[tile_index] = tile_element; - max_height = Math.max( max_height, tile_element.height() ); } tile_index += 1; } - - parent_element.css( "height", max_height ); - this.last_resolution = resolution; this.last_w_scale = w_scale; this.tile_cache = new_tiles; + } +}); + +var LabelTrack = function ( parent_element ) { + Track.call( this, null, parent_element ); + this.container_div.addClass( "label-track" ); +}; +$.extend( LabelTrack.prototype, Track.prototype, { + draw: function() { + var view = this.view, + range = view.high - view.low, + tickDistance = Math.floor( Math.pow( 10, Math.floor( Math.log( range ) / Math.log( 10 ) ) ) ), + position = Math.floor( view.low / tickDistance ) * tickDistance, + width = this.content_div.width(), + new_div = $("<div style='position: relative; height: 1.3em;'></div>"); + while ( position < view.high ) { + var screenPosition = ( position - view.low ) / range * width; + new_div.append( $("<div class='label'>" + position + "</div>").css( { + position: "absolute", + // Reduce by one to account for border + left: screenPosition - 1 + })); + position += tickDistance; + } + this.content_div.children( ":first" ).remove(); + this.content_div.append( new_div ); } }); @@ -209,24 +230,27 @@ this.track_type = "line"; this.height_px = (height ? height : 100); this.container_div.addClass( "line-track" ); + this.content_div.css( "height", this.height_px + "px" ); this.dataset_id = dataset_id; this.cache = new DataCache( "", this ); }; $.extend( LineTrack.prototype, TiledTrack.prototype, { - make_container: function () { - Track.prototype.make_container.call(this); - // console.log("height:", this.height_px); - this.content_div.css( "height", this.height_px ); - }, init: function() { - track = this; - $.getJSON( data_url, { stats: true, track_type: track.track_type, chrom: this.view.chrom, low: null, high: null, dataset_id: this.dataset_id }, function ( data ) { - // console.log(data); + var track = this; + $.getJSON( data_url, { stats: true, track_type: track.track_type, chrom: track.view.chrom, + low: null, high: null, dataset_id: track.dataset_id }, function ( data ) { if (data) { - track.min_value = data['min']; - track.max_value = data['max']; - track.vertical_range = track.max_value - track.min_value; - track.view.redraw(); + if (data == "error") { + track.content_div.addClass("error").text("There was an error in indexing this dataset."); + } else if (data == "no data") { + // console.log(track.content_div); + track.content_div.addClass("nodata").text("No data for this chrom/contig."); + } else { + track.min_value = data['min']; + track.max_value = data['max']; + track.vertical_range = track.max_value - track.min_value; + track.view.redraw(); + } } }); }, @@ -287,43 +311,14 @@ } }); -var LabelTrack = function ( parent_element ) { - Track.call( this, null, parent_element ); - this.container_div.addClass( "label-track" ); -}; -$.extend( LabelTrack.prototype, Track.prototype, { - draw: function() { - var view = this.view, - range = view.high - view.low, - tickDistance = Math.floor( Math.pow( 10, Math.floor( Math.log( range ) / Math.log( 10 ) ) ) ), - position = Math.floor( view.low / tickDistance ) * tickDistance, - width = this.content_div.width(), - new_div = $("<div style='position: relative; height: 1.3em;'></div>"); - while ( position < view.high ) { - var screenPosition = ( position - view.low ) / range * width; - new_div.append( $("<div class='label'>" + position + "</div>").css( { - position: "absolute", - // Reduce by one to account for border - left: screenPosition - 1 - })); - position += tickDistance; - } - this.content_div.children( ":first" ).remove(); - this.content_div.append( new_div ); - } -}); - -var itemHeight = 13, - itemPad = 3, - thinHeight = 7, - thinOffset = 3; - -var FeatureTrack = function ( name, dataset_id ) { +var FeatureTrack = function ( name, dataset_id, height ) { Track.call( this, name, $("#viewport") ); this.track_type = "feature"; + this.height_px = (height ? height : 100); this.container_div.addClass( "feature-track" ); + this.content_div.css( "height", this.height_px + "px" ); this.dataset_id = dataset_id; - this.zo_slots = new Object(); + this.zo_slots = {}; this.show_labels_scale = 0.01; this.showing_labels = false; }; @@ -331,7 +326,7 @@ calc_slots: function( include_labels ) { // console.log("num vals: " + this.values.length); - end_ary = new Array(); + var end_ary = new Array(); var scale = this.container_div.width() / (this.view.high - this.view.low); // console.log(scale); if (include_labels) this.zi_slots = new Object(); diff -r e7b9d15e8e93 -r 62b897ca35ca static/trackster.css --- a/static/trackster.css Tue Sep 29 17:57:45 2009 -0400 +++ b/static/trackster.css Tue Sep 29 21:50:44 2009 -0400 @@ -83,10 +83,18 @@ overflow: hidden; } +.track-content.error { + text-align: center; + padding-top: 30px; + background-color: #600; +} +.track-content.nodata { + text-align: center; + padding-top: 30px; + background-color: #ddd; +} + .loading { - background-image: url("/static/images/loading_large_white_bg.gif"); - background-position: center center; - background-repeat: no-repeat; min-height: 100px; } diff -r e7b9d15e8e93 -r 62b897ca35ca templates/dataset/edit_attributes.mako --- a/templates/dataset/edit_attributes.mako Tue Sep 29 17:57:45 2009 -0400 +++ b/templates/dataset/edit_attributes.mako Tue Sep 29 21:50:44 2009 -0400 @@ -101,13 +101,10 @@ <form name="convert_data" action="${h.url_for( controller='root', action='edit' )}" method="post"> <input type="hidden" name="id" value="${data.id}"/> <div class="form-row"> - <label> - ${_('Convert to')}: - </label> <div style="float: left; width: 250px; margin-right: 10px;"> <select name="target_type"> %for key, value in converters.items(): - <option value="${key}">${value.name[8:]}</option> + <option value="${key}">${value.name}</option> %endfor </select> </div> diff -r e7b9d15e8e93 -r 62b897ca35ca templates/tracks/new_browser.mako --- a/templates/tracks/new_browser.mako Tue Sep 29 17:57:45 2009 -0400 +++ b/templates/tracks/new_browser.mako Tue Sep 29 21:50:44 2009 -0400 @@ -32,10 +32,10 @@ </div> <div class="form-row"> <label for="dataset_ids">Datasets to include: </label> - %for dataset_id, dataset_name in datasets.items(): + %for dataset_id, (dataset_ext, dataset_name) in datasets.iteritems(): <div> <input type="checkbox" id="${dataset_id}" name="dataset_ids" value="${dataset_id}" /> - <label style="display:inline; font-weight: normal" for="${dataset_id}">${dataset_name}</label> + <label style="display:inline; font-weight: normal" for="${dataset_id}">[${dataset_ext}] ${dataset_name}</label> </div> %endfor

1 0

[hg] galaxy 2800: merge
by Nate Coraor 02 Oct '09

02 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/6a066b05c94f changeset: 2800:6a066b05c94f user: Kanwei Li <kanwei(a)gmail.com> date: Tue Sep 29 21:51:51 2009 -0400 description: merge 0 file(s) affected in this change: diffs (1344 lines): diff -r 62b897ca35ca -r 6a066b05c94f test-data/interval2maf_3from28way.maf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/interval2maf_3from28way.maf Tue Sep 29 21:51:51 2009 -0400 @@ -0,0 +1,1301 @@ +##maf version=1 +a score=378218.0 +s hg18.chr1 99287304 223 - 247249719 TCCTCTATGCAAGAGTACACTAGCTATTCTGTGGACAGGAGCCAGACAATGTGAGCTGTACATAAGAATTATTTTTGCAGTGTCAAAAGCCATTCTAGGTGGAATCCAAATCACCACTTGCCTTAGACAGACACCCCCTCAGCTTCACTGCAGGTCCAGAGTCAGCCGAGGCCAGAGAGAGAACCACCAGGAGTGGAAGCAACACTCTCTAGGTTCTCTGCAC +s panTro2.chr1 101234886 223 - 229974691 TCCTCTATGCAAGAGTACACTAGCTATTCTATGGACAGGAGCCAGACAATGTGAGCTGTACATAAGAATTATTTTTGCAGTGTCAAAAGCCATTCTAGGTGGAATCCAAATCACCACTTGCCTTAGACAGACACCCCCTCAGCTTCACTGCAGGTCCAGAGTCAGCCGAGGCCACAGAGAGAACCACCAGGAGTGGAAGCAACACTCTCTAGGTTCTCTGCAC + +a score=10640.0 +s hg18.chr1 99287270 34 - 247249719 GCTGTAAGATGCCATGTATTTTGTGATTCTACAA +s panTro2.chr1 101234852 34 - 229974691 GCTGTAAGATGCCATGTATTTTGTGATTCTACAA + +a score=43023.0 +s hg18.chr1 99287229 41 - 247249719 AGGGCCCAGAGGATCTGGCCATGTTCTCATGGCATCATTGA +s panTro2.chr1 101234811 41 - 229974691 AGGGCCCAGAGGATCTGGCCATGTTCTCATGGCATCATTGA + +a score=120618.0 +s hg18.chr1 99287139 90 - 247249719 TCCTTGAAAGGGAAAGACTCTAAAACTTTTCTCTGAATTATGGCCCTGCCACCCCAGCTGGGTTTTTCTCTCAAAGGGAGACAGTAATGA +s panTro2.chr1 101234721 90 - 229974691 TCCTTGAAAGGGAAAGACTCTAAAACTTTTCTCTGAATTACGGCCCTGCCACCCCAGCTGGGTTTTTCTCTCAAAGGGAGACAGTAATGA + +a score=39239.0 +s hg18.chr1 147984545 50 + 247249719 AGAAAAACTTTAGTGGAAACAACCAGTACTTAAAGACCATTTTATGAGGC +s panTro2.chr1 128764240 50 + 229974691 AGAAAAACTTTAGTGGAAACAACCAGTACTTAAAGACCATTTTATGAGGC +i panTro2.chr1 C 0 C 0 + +a score=93901.0 +s hg18.chr1 147984595 35 + 247249719 TGTCATTTACGTATTATCTCTTTTGCTGTTTTTGT +s panTro2.chr1 128764290 35 + 229974691 TGTCATTTACATATTATCTCTTTTGCTGTTTTTGT +i panTro2.chr1 C 0 C 0 + +a score=-5867.0 +s hg18.chr1 99171300 19 - 247249719 CGTGGGGAGAACTGCGCTG +s panTro2.chr1 101114588 19 - 229974691 CGGGGGGAGAACTGCGCTG + +a score=-4312.0 +s hg18.chr1 99171258 42 - 247249719 GGGAAATGACCACCTCGGCCTCGCCGGGGTTCTGCGGACAAA +s panTro2.chr1 101114546 42 - 229974691 GGGAAATGACCACCTCGGCCTCGCCGGGGTTCTGCGGGCAAA + +a score=-5717.0 +s hg18.chr1 99171247 11 - 247249719 CCGGCTAGGGA +s panTro2.chr1 101114535 11 - 229974691 CCGGCTAGGGA + +a score=-26975.0 +s hg18.chr1 99171193 54 - 247249719 GAGCGCCACACGCCCGTGCTTCGCGCCCAAACCGGCCTCACCCGGCGCGGCCAT +s panTro2.chr1 101114481 54 - 229974691 GAGCGCCACACGCCCGTGCTTCGCGCCCAAACCGGCCTCACCCGGCGCGGCCAT + +a score=-60785.0 +s hg18.chr1 99171137 56 - 247249719 ACTAGGGGGACGCTCAGGGCTCGCGGTCCTGAGCGCGGCTGGCCTTTGCGGAAGTG +s panTro2.chr1 101114425 56 - 229974691 ACTAGGGGGACGCTCAGGGCTCGCGGTCCTGAGCGCGGCTGGCCTTTGCGGAAGTG + +a score=151634.0 +s hg18.chr1 148185136 140 + 247249719 acgtctgtaatcccagctactcgtgaggctgatgcaggagaatcacttgaacctgggaagtggaggttgctgtgagccaagattgtgccactgcatttcagcctggctgacagagcaagacttcctctgaaaaaaaaaaa +s panTro2.chr1 128947445 139 + 229974691 acgtctgtaatcccagctactcgtgaggctaatgcaggagaatcacttgaacctgggaagtggaggttgctgtgagccaagattgtgccactgcatttcagcctgggtgacagagcaagacttcctctg-gaaaaaaaaa +i panTro2.chr1 C 0 C 0 + +a score=518150.0 +s hg18.chr10 80123058 56 - 135374737 ACAATATTGTCGAGGGAACTGAAAAACAATCTCACAGTCAATCTACTTCACTGTAA +s mm8.chr10 74075614 56 + 129959148 TTAGAGTTGTTGAGGGAATTGACGTGCAACCTCACAGTCAATCAACATCTTTGTAA +s panTro2.chr10 82310642 56 - 135001995 ACAATATTGTCGAGGGAACTGAAAAACAATCTCACAGTCAATCTACTTCACTGTAA + +a score=200210.0 +s hg18.chr10 80122998 60 - 135374737 TGTGCCCTTCAGAAGTAACAAATATGGAAATCACATCTGAACAAAACAAGGGGAGTTTGA +s panTro2.chr10 82310582 60 - 135001995 TGTGCCCTTCGGAAGTAACAAATATGGAAATCACATTTGAACAAAACAAGGAGAATTTGA +s mm8.chr10 74075554 60 + 129959148 TTTGCCCTGCAGAGAAAACAGGCATGAAAATCACACATGACCAGAGCCAGGAAACGTTGG + +a score=136193.0 +s hg18.chr10 80122957 41 - 135374737 AAAAAACTATCTACGCACAAATGTTTCAGAACTTCAAACTA +s panTro2.chr10 82310541 41 - 135001995 AAAAAACTATCTACGCACAAATGTTTCAGAACTTCAAACTA +s mm8.chr10 74075513 41 + 129959148 AAAAAACTGCCCACCTGCAGATCCCTCAAAACTACACACGT + +a score=1023171.0 +s hg18.chr10 80122882 75 - 135374737 AAAAGGCATCCTCAGACACGTTAAAAACTTAGCAGAACTTGAAAAATCAGTAGCTAACATGTACAGTCAAATAGA +s panTro2.chr10 82310466 75 - 135001995 AAAAGGCATCCTCAGACATGTTAAAAACTTAGCAGAACTTGAAAAATCAGTAGCTAACATGTACAGTCAAATAGA +s mm8.chr10 74075438 75 + 129959148 AAAAGGGATCCTCAGACATGTGAAAAACTTGGCAGAGCTCGAGAAATCAGTGTCTAACATGTACAGTCACATAGA + +a score=-29743.0 +s hg18.chr10 80122851 31 - 135374737 CAGTGTGTAAAACAGACCCTCAGAGAGAACC +s panTro2.chr10 82310435 31 - 135001995 CAGTGTGTAAAACAGACCCTCAGAGAGAACC +s mm8.chr10 74075407 31 + 129959148 CGCAGTGGGGGGCAGAACCCCACAGACATCC + +a score=121521.0 +s hg18.chr10 80122808 43 - 135374737 GCCGAGAAAATTAAGTCCTCTATGACACAGCTATCAACAACGA +s panTro2.chr10 82310392 43 - 135001995 GCCGAGAAAATTAAGTCCTCTATGACACAGCTATCAACAACGA +s mm8.chr10 74075364 40 + 129959148 GCCAGAGAAACCA---CGTCTACGACACAGCCACCAGCATCCA + +a score=101339.0 +s hg18.chr10 80122748 60 - 135374737 TTTCTGTCCACAGAGTGTGTCTGTATAACAGGTGTTAAATGCACGACCAACTTGATGCCT +s panTro2.chr10 82310332 60 - 135001995 TTTCTGTCCACAGAGTGTGTCTGTATAACAGGTGTTGAATGCACGACCAACATGATGCCT +s mm8.chr10 74075304 60 + 129959148 ATTCCATCCACAGACAGCATCTCTGCACCAGCTGCTAAATGCACTGCCAGTGCCACACAC + +a score=153575.0 +s hg18.chr10 80122616 132 - 135374737 cctcctcctACATTTTTTCCACTTTCCGTTTCAACGTCTGGTCCCCCAACA------------ccacctcttctacctccatttccaactcctcttcctccaccacctccttctattccttgccctccacctccttcAGCTTCA +s panTro2.chr10 82310207 125 - 135001995 -------ctACATTTTTTCCACTTTCCATTTCAACGTCTGGTCCCCCAACA------------ccacctcttctacctccatttccaactcctcttcctccaccacctccttctattccttgccctccacctccttcAGCTTCA +s mm8.chr10 74075167 137 + 129959148 ----ccccacaacttgttacattttctcttcccatttctacaccccctacttcttctctacctcttcctcctccactgtcacttcctcctc---ctcctcGGCCACCAGCTCCCCGCCTCTTCCCACAGCCTCCTTCCACGTCC + +a score=-80842.0 +s hg18.chr10 80122576 40 - 135374737 ttgtcctcctccctctcctccttctatccctcttcctctt +s panTro2.chr10 82310184 23 - 135001995 ttgtcctcctccctctcctcctt----------------- +s mm8.chr10 74075144 23 + 129959148 cctttctccccctaaccctcctc----------------- + +a score=15475.0 +s hg18.chr10 80122507 69 - 135374737 tcctccttctcctcctcctgctcctgctcctcttgctcctcctcctgacatttctcctttttctctttt +s mm8.chr10 74075096 48 + 129959148 tccgcctcttcctagacct---------------------cccattgcctttaccacttttcctcttcc +s panTro2.chr10 82310115 69 - 135001995 tcctccttctcctcctcctgctcctgctcctcttgctcctcctcctgacatttctcctttttctctttt + +a score=-32513.0 +s hg18.chr10 80122465 42 - 135374737 CTCTCCTTCTGCCTGtccccttccccctcctcctcctatttc +s mm8.chr10 74075078 18 + 129959148 CTC------------------------TGctcccctcccaca +s panTro2.chr10 82310073 42 - 135001995 CTCTCCTTCTGCCTGtccccttcctcctccttctcctatttc + +a score=286554.0 +s hg18.chr10 80122411 54 - 135374737 ACCTATTGAAACCGAAAGAAATATTTTTGAAAATTTTGCCCATCCACCAAACAT +s panTro2.chr10 82310019 54 - 135001995 ACCTGTTGAAACCGAAAGAAATATGTTTGAAAATTTTGCCCATCCACCAAACAT +s mm8.chr10 74075024 54 + 129959148 AGATACAGAACCAAAAAGGAACTCTTTTGAGATCGCTCCCCATCCACCTAGCAT + +a score=1014462.0 +s hg18.chr10 80122238 173 - 135374737 CCCAGGCCTCACTTCTCATTCTCCACTTTGCCAACTGTTTCAAGAACTGTGGAACTCAAATCAGAACCTAATGTCATCAGTTCTCCTGCTGAGTGTTCCTTGGAACTTTCTCCTT---CAAGGCCTTGTGTTTTACATTCTTCACTCTCTAGGAGAGAGACACCTATTTGTATGTT +s mm8.chr10 74074848 176 + 129959148 TCTTGGTCTCACTTTTCTTTCTCAACTCTGCCAACGATTTCCAGAGCGGTGGAACTCGGGTCGGAACCTAATGTGGTCACTTCTCCCGCTGACTGCACCTTGGAACTTTCTCCTCCTCTGAGACCCCGTATTTTAAACTCCTTAAGCTCTAAGAGAGAGACTCCCACATGTGCATC +s panTro2.chr10 82309846 173 - 135001995 CCCAGGCCTCACTTCTCATTCTCCACTTTGCCAACTGTTTCAAGAACTGTGGAACTCAAATCAGAACCTAATGTCATCAGTTCTCCTGCTGAGTGTTCCTTGGAACTTTCTCCTT---CAAGGCCTTGTGTTTTAAATTCTTCACTCTCTAGGAGAGCGACACCTATTTGTATGTT + +a score=337224.0 +s hg18.chr10 80122083 155 - 135374737 GAATCTGTACAAACAAAAGAGGTAGCAGCAATCCATTGCTTACAACTGAAGAGGCAAATTTGACAGAGAAAGAGGAAATAAGGCAAGGTGAAACACTGATGATAGAAGGAACAGAACAGTTGAAATCTCTCTCTTCAGACTCTTCATTTTGCTTT +s panTro2.chr10 82309691 155 - 135001995 GAATCTGTACAAACAAAAGAGGTAGCAGCAATCCATTGCTTACAACTGAAGAGGCAAATTTGACAGAGAAAGAGGAAATAAGGCAAGGTGACACACTGATTATGAAAGGAAGAGAACAGTTGAAATCTCTCTCTTCAGACTCTTCATTTTGCTTT +s mm8.chr10 74074696 152 + 129959148 GATGCCACCCAAGCCAGAGAGGTAGCAGCAACGTTCTGCTGGCAACTGAAGATGCCCACGAGTCAGAGAA---AGAAGGGGGACACAGAGACACCCTAATCGTCCAGCAAACAGAGCAGCTGAAATCTCTGTCTTCTGGCTCTTCTTTTTCCTCC + +a score=196272.0 +s hg18.chr10 80122035 48 - 135374737 TGCAGCAGTGGCAAGGCACCAGGCAGAAAGCTGAAAATGAAAACACTG +s panTro2.chr10 82309643 48 - 135001995 TGCAGCAGTGGCAAGGCACCAGGCAGAAAGCTGAAAATGAAAACACTG +s mm8.chr10 74074648 48 + 129959148 TGGTGGAGTGGCAGATCACCAATCAGAGAGCTGAATGCGAAAGCGCCA + +a score=267386.0 +s hg18.chr10 80121994 41 - 135374737 GCTGATGAGGAAAGTTCCAAATAGACCAGAGATCATAGATC +s panTro2.chr10 82309602 41 - 135001995 GCTGATGAGGAAAGTTCCAAATAGACCAGAGATCATAGATC +s mm8.chr10 74074607 41 + 129959148 GCTCATGTGGAAAGCCCCAAACAGGCCAGAGACCATAGACC + +a score=799420.0 +s hg18.chr10 80121885 109 - 135374737 ATTTTGTAGACCCATTTTCACCCAAAATACAAGCCAAGAGTAAGTCTCTGAGGGGCCCAAGAGAAAAGATTCAGAGGCTGTGGAGTCAGTCAGTCAGCTTACCCAGGAG +s panTro2.chr10 82309493 109 - 135001995 ATTTTGTAGACCTATTTTCACCCAAAGTACAAGCCAAGAGTAAGTCTCTGAGGGGCCCAAGAGAAAAGATTCAGAGGCTGTGGAGTCAGTCAGTCAGCTTACCCAGGAG +s mm8.chr10 74074498 109 + 129959148 ATTTTGAAGAGCTGTTGGCACCCAGAACACAAGTTAAGAGTCAGTCTCTGAGGGGCCCAAGAGAAAAGATCCAGAGGGTGTGGAATCAGTCTGTGAGCTTTCCTAGGCG + +a score=212883.0 +s hg18.chr10 80121842 43 - 135374737 ATAAGTCAAGTATCAACAAATTCAGACATTTCACAGAGAACAG +s panTro2.chr10 82309450 43 - 135001995 ATAAGTCAAGTATCAACAAATTCAGACATTTCACAGAGAACAG +s mm8.chr10 74074455 43 + 129959148 ATAGGTCAAAGGTCAACAAACTCAGACCTTCAGCCACGAACAG + +a score=804771.0 +s hg18.chr10 80121755 87 - 135374737 AGCAACAAACTGAAGTCTGCAAGAAAATTCACATTTCTATCTGATGAGGATGACTTAAGTGCCCATAATCCCCTTTATAAGGAAAAC +s panTro2.chr10 82309363 87 - 135001995 AGCAACAAACTGAAGGCTGCAAGAAAATTCACATTTCTATCTGATGAGGATGACTTAAGTGCCCATAATCCCCTTTATAAGGAAAAC +s mm8.chr10 74074368 87 + 129959148 GAGAGCCAGCCTAACCCAGCAAGGACGTTCTCATTTGTTCCTGATGAGGATAACTTAAGTACCCATAATCCCCTTTACATGGAAAGT + +a score=2273365.0 +s hg18.chr10 80121613 142 - 135374737 TCTTTTCCTTCTCTACCATTTTCAACAAAGCAGGGGAAATAACTCAGTCTCAGAAGACAGGAAACATCAACAAGTTGTGATGCCCTTTTCTTCCAATACTATTGAGGCTCACAAGTCAGCTCATGTAGACGGATCACTTAAG +s panTro2.chr10 82309221 142 - 135001995 TATTTTCCTTCTCTACCATTTTCAACAAAGCAGGGGAAATAACTCAGTCTCAGAAGACAGGAAACATCAACAAGTTGTGATGCCCTTTTCTTCCAATACTATTGAGGCTCACAAGTCAGCTCATGTAGACGGATCACTTAAG +s mm8.chr10 74074226 142 + 129959148 TCTTTTCCTTCTCTACCATTTTGAACAAAGCAGGGGAAATAACTCAGTCCCAGAAGACAGGAGCAGTCATCGCGATGGGATGGCCTTTTCCTCCAGTACCACTGAGTCTCATGAGCCAGCTCATGTAGAGGGACCACTTAAG + +a score=591281.0 +s hg18.chr11 18327947 30 - 134452384 GCCTACAAATGGAGTGTTGAGGATATGTAA +s mm8.chr9 46049473 30 + 124000669 GCCTACAAGTGGAGTGTGGAGGATATGTGA +s panTro2.chr11 18640018 30 - 134204764 GCCTACAAATGGAGTGTTGAGGATATGTAA + +a score=887677.0 +s hg18.chr11 18327884 63 - 134452384 TCCAATGGATTTGAACAGAAGCGCTTTGCCAGGCTTGCCAGCAAGAAGGCAGTGGAGGAACTT +s panTro2.chr11 18639955 63 - 134204764 TCCAATGGATTTGAACAGAAGCGCTTTGCCAGGCTTGCCAGCAAGAAGGCAGTGGAGGAACTT +s mm8.chr9 46049410 63 + 124000669 TCCAATGGCTTTGAACAGAAGCGCTTTGCCAGGCTCGCCAGCAAGAAGGCTGTGGAGGAGCTT + +a score=63327.0 +s hg18.chr11 18327883 1 - 134452384 A +s panTro2.chr11 18639954 1 - 134204764 A +s mm8.chr9 46049409 1 + 124000669 A + +a score=156152.0 +s hg18.chr11 116206508 6 + 134452384 ATGCAG +s mm8.chr9 78014961 6 - 124000669 ATGCAG +i mm8.chr9 C 0 C 0 +s panTro2.chr11 115648111 6 + 134204764 ATGCAG +i panTro2.chr11 C 0 C 0 + +a score=204572.0 +s hg18.chr11 116206514 49 + 134452384 CCCCGGGTACTCCTTGTTGTTGCCCTCCTGGCGCTCCTGGCCTCTGCCC +s panTro2.chr11 115648117 49 + 134204764 CCCCGGGTACTCCTTGTTGTTGCCCTCCTGGCGCTCCTGGCCTCTGCCC +i panTro2.chr11 C 0 C 0 +s mm8.chr9 78014967 49 - 124000669 CCCCGGACGCTCCTCACTGTGGCCCTCTTGGCTCTCCTGGCATCTGCCC +i mm8.chr9 C 0 C 0 + +a score=27414.0 +s hg18.chr11 18240627 24 - 134452384 ACTAAGAAGCTCAACACCCAGTGA +s panTro2.chr11 18551568 24 - 134204764 ACTAAGAAGCTCAACACCCAGTGA +s mm8.chr9 45981373 24 + 124000669 AGCGAGACTCTGACTGCCCAGTGA + +a score=65817.0 +s hg18.chr11 18240590 37 - 134452384 CTTCAAGGTCAGCTTCCTGAGCGCTCTCGAGGAGTAC +s panTro2.chr11 18551531 37 - 134204764 CTTCAAGGTCAGCTTCCTGAGCGCTCTCGAGGAGTAC +s mm8.chr9 45981336 37 + 124000669 GCTTAAGACCCAAGTCCAGAGTGTGATCGACAAGGCC + +a score=121894.0 +s hg18.chr11 18240544 46 - 134452384 CCGCGCTCGAGGACCTCCGCCAAGGCCTGCTGCCCGTGCTGGAGAG +s mm8.chr9 45981290 46 + 124000669 CTGCGCTGGAGGACCTGCGCCATAGTCTGATGCCCATGCTGGAGAC +s panTro2.chr11 18551485 46 - 134204764 CCGCGCTCGAGGACCTCCGCCAGGGCCTGCTGCCCGTGCTGGAGAG + +a score=368735.0 +s hg18.chr11 18240366 178 - 134452384 GACCGCGCGCGCGCCCATGTGGACGCGCTGCGCACGCATCTGGCCCCCTACAGCGACGAGCTGCGCCAGCGCTTGGCCGCGCGCCTTGAGGCTCTCAAGGAGAACGGCGGCGCCAGACTGGCCGAGTACCACGCCAAGGCCACCGAGCATCTGAGCACGCTCAGCGAGAAGGCCAAGC +s panTro2.chr11 18551307 178 - 134204764 GACCGCGCGCGCGCCCATGTGGACGCGCTGCGCACGCATCTGGCCCCCTACAGCGACGAGCTGCGCCAGCGCTTGGCCGCGCGCCTTGAGGCTCTCAAGGAGAACGGCGGCGCCAGACTGGCCGAGTACCACGCCAAGGCCACCGAGCATCTGAGCACGCTCAGCGAGAAGGCCAAGC +s mm8.chr9 45981118 172 + 124000669 GACCGCATGCGCACACACGTAGACTCTCTGCGCACACAGCTAGCGCCCCACAGCGAACAGATGCGCGAGAGCCTGGCCCAGCGCCTGGCTGAGCTCAAGA------GCAACCCTACCTTGAACGAGTACCACACCAGGGCCAAAACCCACCTGAAGACACTTGGCGAGAAAGCCAGAC + +a score=97575.0 +s hg18.chr11 18240323 43 - 134452384 CGAGCTGCAAGAGAAGCTGAGCCCACTGGGCGAGGAGATGCGC +s panTro2.chr11 18551264 43 - 134204764 CGAGCTGCAAGAGAAGCTGAGCCCACTGGGCGAGGAGATGCGC +s mm8.chr9 45981075 43 + 124000669 GGAGCTGCAAGGGAGACTGTCCCCTGTGGCTGAGGAATTTCGC + +a score=580950.0 +s hg18.chr11 18240123 200 - 134452384 CAGGAGTTCTGGGATAACCTGGAAAAGGAGACAGAGGGCCTGAGGCAGGAGATGAGCAAGGATCTGGAGGAGGTGAAGGCCAAGGTGCAGCCCTACCTGGACGACTTCCAGAAGAAGTGGCAGGAGGAGATGGAGCTCTACCGCCAGAAGGTGGAGCCGCTGCGCGCAGAGCTCCAAGAGGGCGCGCGCCAGAAGCTGCA +s panTro2.chr11 18551064 200 - 134204764 CAGGAGTTCTGGGATAACCTGGAAAAGGAGACAGAGGGCCTGAGGCAGGAGATGAGCAAGGATCTGGAGGAGGTGAAGGCCAAGGTGCAGCCCTACCTGGACGACTTCCAGAAGAAGTGGCAGGAGGAGATGGAGCTCTACCGCCAGAAGGTGGAGCCGCTGCGCGCCGAGCTCCAAGAGGGCGCGCGCCAGAAGCTGCA +s mm8.chr9 45980875 200 + 124000669 CGGGACTTCTGGGATAACCTGGAGAAAGAAACAGATTGGGTGAGACAGGAGATGAACAAGGACCTAGAGGAAGTGAAACAGAAGGTGCAGCCCTACCTGGACGAATTCCAGAAGAAATGGAAAGAGGATGTGGAGCTCTACCGCCAGAAGGTGGCGCCTCTGGGCGCCGAGCTGCAGGAGAGCGCGCGCCAGAAGCTGCA + +a score=49052.0 +s hg18.chr11 18240102 21 - 134452384 GAACAGCTCGGCCCTGTGACC +s panTro2.chr11 18551043 21 - 134204764 GAACAGCTCGGCCCTGTGACC +s mm8.chr9 45980854 21 + 124000669 GAACGGCTGGGCCCATTGACT + +a score=167437.0 +s hg18.chr11 18240047 55 - 134452384 CCTAAAGCTCCTTGACAACTGGGACAGCGTGACCTCCACCTTCAGCAAGCTGCGC +s panTro2.chr11 18550988 55 - 134204764 CCTAAAGCTCCTTGACAACTGGGACAGCGTGACCTCCACCTTCAGCAAGCTGCGC +s mm8.chr9 45980799 55 + 124000669 CCTGAATCTCCTGGAAAACTGGGACACTCTGGGTTCAACCGTTAGTCAGCTGCAG + +a score=-14919.0 +s hg18.chr11 1812377 30 + 134452384 ATGCTCCACCTGCATGGCTGGCAAACCATG +s mm8.chr7 142247071 26 + 145134094 ----CCAACTGGACTACCGTGTAGAAGATG +i mm8.chr7 C 0 C 0 +s panTro2.chr11 1858435 30 + 134204764 ATGCTCCACCTGTATGGCTGGCAAACCACG +i panTro2.chr11 C 0 C 0 + +a score=117382.0 +s hg18.chr12 93909439 1 - 132349534 A +s panTro2.chr12 50116182 1 + 135371336 A +s mm8.chr15 12392656 1 - 103492577 A + +a score=2422168.0 +s hg18.chr12 93909303 136 - 132349534 AAATTGAATCACTCTTTGACAACAGGCTATGTACATGTGGCACTTCAGATTCTGATGAAGGGAGATATATTGAATATATTCGGGTAAAGGGAAGTAACTATCATCTTTCTGACAATGATGCTTCTGATGTGGAATA +s panTro2.chr12 50116046 136 + 135371336 AAATTGAATCACTCTTTGACAACAGGCTATGTACATGTGGCACTTCAGATTCTGATGAAGGGAGATATATTGAATATATTCGGGTAAAGGGAAGTAACTATCATCTTTCTGACAATGATGCTTCTGATGTGGAATA +s mm8.chr15 12392520 136 - 103492577 AAATCGAATCGCTCTTTGACCACCGGCTATGTTCATGTGGCGCTGCCGACTCGGATGAAGGGAGGTACATTGAGTACATCCGCGTGAAGGGAAGCAACTATCATCTCTCCGACAACGACGCTTCTGACGTGGAGTA + +a score=1478304.0 +s hg18.chr12 93909213 90 - 132349534 GAGCTTTCTTCCTCTATGCTGGATTTGCTGCTGTGGGACTCCTTTTCATCTATGGCTGTCTTCCTGAGACCAAAGGCAAAAAATTAGAGG +s panTro2.chr12 50115956 90 + 135371336 GAGCTTTCTTCCTCTATGCTGGATTTGCTGCTGTGGGACTCCTTTTCGTCTACGGCTGTCTTCCTGAGACCAAAGGCAAAAAATTAGAGG +s mm8.chr15 12392430 90 - 103492577 GAGCATTCTTCCTCTACGCCGGATTCGCCGCTGTGGGACTGCTTTTTGTCTATGGCTGCCTCCCTGAAACCAAGGGGAAAAAATTGGAGG + +a score=129525.0 +s hg18.chr13 112381694 1 + 114142980 A +s panTro2.chr13 114131566 1 + 115868456 A +i panTro2.chr13 C 0 C 0 +s mm8.chr8 12748309 1 + 132085098 A +i mm8.chr8 C 0 C 0 + +a score=39963.0 +s hg18.chr13 112381695 121 + 114142980 TGAACTCACCAGAGGCGAGGCTCTGCGTTGCTCAATGCAGAGACTCTTACCCAGGGTGTCAGCCTCTGAAAGATACACGTGCCTGGGCCTCTTCCCTGAAGATGGACCCGGCAGGTCTGGA +s panTro2.chr13 114131567 121 + 115868456 TGAACTCACCAGAGGCGAGGCTCTGCGTTGCTCAATGCAGAGACTCTTACCCAGGGTGTCAGCCTCTGAAAGATACACGTGCCTGGGCCTCTTCCCTGAAGATGGACCCGGCAGGTCTGGA +i panTro2.chr13 C 0 C 0 +s mm8.chr8 12748310 91 + 132085098 TTTGTTCACCAGAGT----GTCCTGGCCTCCTGCCTATGTGGACTCATTCCCAAGG-ACCAGCCT-TGAAGGACGCA-ATGTAGGG-----CTCCATGGA------------------GGA +i mm8.chr8 C 0 C 0 + +a score=1055.0 +s hg18.chr13 112381816 44 + 114142980 GGGAGGCCCCCGTGATGAATCCCGTGATGAGCCGCCGATCCGAG +s panTro2.chr13 114131688 44 + 115868456 GGGAGGCCCCTGTGATGAATCCCGTGATGAGCCGCTGATCCGAG +i panTro2.chr13 C 0 C 0 +s mm8.chr8 12748401 15 + 132085098 GGGAGGTCTGTGTGA----------------------------- +i mm8.chr8 C 0 C 0 + +a score=-16674.0 +s hg18.chr13 112381860 93 + 114142980 CTCAGGCTGCGTCATGGGACCAGCCACAAGGTTGCCTGACC-TATAAAGGTCGCAGGAGTGCCTCAGGGACACAGAAGCAGTTACAGCTGCCAG +s panTro2.chr13 114131732 93 + 115868456 CTCGGGCTGCGTCATGGGACCAGCCACAAGGTTGCCTGACC-TATAAAGGTCACAGGAGTGCCTCAGGGAGACAGAAGCAGTTACAGCTGTCAG +i panTro2.chr13 C 0 C 0 +s mm8.chr8 12748416 81 + 132085098 -----------CACTGGGACTTGCCACAGGTCAG--TGATTGTTCAGAGGTCACAGGAGTGCCACCCTCAGGCAGAGTCATCTGTCTTTTCCAG +i mm8.chr8 C 0 C 0 + +a score=1627846.0 +s hg18.chr14 7658261 84 - 106368585 ACCCTGGAGAAACACATGAAAAAGTGGCACGGCGAGCACTTGCTGACTAACGACGTCAAAATCGAGCAGGCCGAGAGGAGCTAA +s panTro2.chr14 7807052 84 - 107349158 ACCCTGGAGAAACACATGAAAAAGTGGCACGGCGAGCACTTGCTGACTAACGACGTCAAAATCGAGCAGGCCGAGAGGAGCTAA +s mm8.chr12 12099869 84 - 120463159 ACCCTGGAGAAACACATGAAAAAGTGGCACGGTGAACACTTGCTGACTAATGATGTCAAAATCGAGCAGGCTGAGAGGAGCTAA + +a score=2813413.0 +s hg18.chr14 7658104 157 - 106368585 GCGGAGCCACACCGGCGAGCGGCCTTACAAGTGCGAGCTGTGCAACTACGCGTGCGCGCAGAGCAGCAAGCTCACGCGCCACATGAAGACGCACGGGCAGATCGGCAAGGAGGTGTACCGCTGCGACATCTGCCAGATGCCCTTCAGCGTCTACAGC +s panTro2.chr14 7806895 157 - 107349158 GCGGAGCCACACCGGCGAGCGGCCTTACAAGTGCGAGCTGTGCAACTACGCGTGCGCGCAGAGCAGCAAGCTCACGCGCCACATGAAGACGCACGGGCAGATCGGCAAGGAGGTGTACCGCTGCGACATCTGCCAGATGCCCTTCAGCGTCTACAGC +s mm8.chr12 12099712 157 - 120463159 GAGGAGCCACACCGGCGAGCGGCCTTACAAGTGCGAGCTGTGCAACTACGCGTGCGCGCAGAGCAGCAAGCTCACGCGCCACATGAAGACGCACGGGCAGATCGGCAAGGAGGTGTACCGCTGCGACATCTGCCAGATGCCCTTCAGCGTCTACAGC + +a score=1778334.0 +s hg18.chr14 7657988 116 - 106368585 CCGCACCTgggcggcccgggccccgggcggcccAGCTCCAAGGAGGGCCGCCGCAGCGACACGTGCGAGTACTGCGGCAAGGTGTTCAAGAACTGCAGCAACTTGACGGTGCACCG +s panTro2.chr14 7806779 116 - 107349158 CCGCACCTgggcggcccgggccccgggcggcccAGCTCCAAGGAGGGCCGCCGCAGCGACACGTGCGAGTACTGCGGCAAGGTGTTCAAGAACTGCAGCAACTTGACGGTGCACCG +s mm8.chr12 12099596 116 - 120463159 CCTCACCTGGGTGGTCCGGGTCCTGGGAGGCCGAGCTCCAAGGAGGGCCGCCGCAGCGACACATGTGAGTACTGCGGCAAGGTCTTCAAGAACTGTAGCAACCTGACGGTGCACCG + +a score=448798.0 +s hg18.chr14 7657957 31 - 106368585 CCGCAGCGGCACGGCCAGCGGAGGCAGCACC +s panTro2.chr14 7806748 31 - 107349158 CCGCAGCGGCACGGCCAGCGGGGGCAGCACC +s mm8.chr12 12099565 31 - 120463159 GCGCAGTGGCACGGCGAGCGGGGGCAGCACA + +a score=951272.0 +s hg18.chr14 7657896 61 - 106368585 AGAACGGCAGCCTGCGCTTCTCCACGCCGCCCGGGGACCTGCTGGACGGCGGCCTCTCGGG +s panTro2.chr14 7806687 61 - 107349158 AGAACGGCAGCCTGCGCTTCTCCACGCCGCCCGGGGACCTGCTGGACGGCGGCCTCTCGGG +s mm8.chr12 12099504 61 - 120463159 AGAACGGCAGCCTGCGCTTCTCAACGCCACCCGGGGACCTGCTGGACGGCGGGCTGTCCGG + +a score=2903485.0 +s hg18.chr14 7657646 250 - 106368585 GAGCCCTTCCCCGGGCTCTTCCCGCGCAAGCCCGCGCCGCTGCCCAGCCCCGGGCTCAACAG------------CGCCGCCAAGCGCATCAAGGTGGAGAAGGACCTGGAGCTGCCGCCCGCCGCGCTCATCCCGTCCGAGAACGTGTACTCGCAGTGGCTGGTGGGCTACGCGGCGTCGCGGCACTTCATGAAGGACCCCTTCCTGGGCTTCACGGACGCACGACAGTCGCCCTTCGCCACGTCGTCCGAGCACTCGTCCG +s panTro2.chr14 7806437 250 - 107349158 GAGCCCTTCCCCGGGCTCTTCCCGCGCAAGCCCGCGCCGCTGCCCAGCCCCGGGCTCAACAG------------CTCCGCCAAGCGCATCAAGGTGGAGAAGGACCTGGAGCTGCCGCCCGCCGCGCTCATCCCGTCCGAGAACGTGTACTCGCAGTGGCTGGTGGGCTACGCGGCGTCGCGGCACTTCATGAAGGACCCCTTCCTGGGCTTCACGGACGCACGACAGTCGCCCTTCGCCACGTCGTCCGAGCACTCGTCCG +s mm8.chr12 12099242 262 - 120463159 GAGCCCTTTCCAGCTCTCTTCCCACGCAAGCCAGCACCGCTGCCCAGCCCTGGGCTCGGTGGTCCCGCGCTGCACGCGGCCAAGCGCATCAAGGTGGAGAAAGACCTGGAGCTGCCACCTGCCGCCCTCATCCCATCTGAGAACGTGTACTCGCAGTGGCTCGTGGGCTACGCAGCATCGCGCCACTTCATGAAGGACCCATTCCTGGGCTTCACGGATGCGCGCCAGTCGCCTTTCGCCACATCGTCGGAACATTCCTCTG + +a score=152242.0 +s hg18.chr14 7657593 53 - 106368585 cgggcgcgggcggcgcggtcaacgggcgcgggggcggCTTCGCGCCAGGCACC +s panTro2.chr14 7806384 53 - 107349158 cgggcgcgggcggcgcggtcaacgggcgcgggggcggCTTCGCGCCAGGCACC +s mm8.chr12 12099189 53 - 120463159 CGGGTGCACCGGGTGCAGTGAACGGGCGCGGCGGGGCCTTCGCGCCAGGCGCA + +a score=564664.0 +s hg18.chr14 7657449 144 - 106368585 AGGTCATGGAGAACGTGGGCCTAGGCGCACTGCCGCAGTACGGCGAGCTCCTGGCCGACAAGCAGAAGCGCGGCGCCTTCCTGAAGCGTGCggcgggcggcggggacgcgggc---gacgacgacgacgcgggcggctgcggggacg +s panTro2.chr14 7806240 144 - 107349158 AGGTCATGGAGAACGTGGGCCTAGGCGCACTGCCGCAGTACGGCGAGCTCCTGGCCGACAAGCAGAAGCGCGGCGCCTTCCTGAAGCGTGCggcgggcggcggggacgcgggc---gacgacgacgacgcgggcggctgcggggacg +s mm8.chr12 12099075 114 - 120463159 AGGTGATGGAGGACGCAGGGCTGGGCGCACTGCCGCAGTATGGGGAG------------------AAGCGGGGCGCCTTCCTGAAGCGTGCAGGC---------------GACACGGGTGATGCCGGAGCTGTTGGCTGTGGGGACG + +a score=158337.0 +s hg18.chr14 7657397 52 - 106368585 gggggcggcgcggccAAGGCGCTGGCTGACGAGAAGGCGCTGGTGCTGGGCA +s panTro2.chr14 7806188 52 - 107349158 gggggcggcgcggccAAGGCGCTGGCTGACGAGAAGGCGCTGGTGCTGGGCA +s mm8.chr12 12099026 49 - 120463159 GGGGC---TGCAGCTGCGGCTCTGGCGGATGAGAAGGCTCTGGCCCTGGGCA + +a score=706451.0 +s hg18.chr14 7657293 104 - 106368585 TACTGGAGAACGAGAGCCGGCCCGAGTCGAGCTTCAGCATGGACTCGGAGCTGAGCCGCAACCGCGAGAACGGCGGTGGTGGGGTgcccggggtcccgggcgcg +s panTro2.chr14 7806084 104 - 107349158 TACTGGAGAACGAGAGCCGGCCCGAGTCGAGCTTCAGCATGGACTCGGAGCTGAGCCGCAACCGCGAGAACGGCGGTGGTGGGGTgcccggggtcccgggcgcg +s mm8.chr12 12098922 104 - 120463159 TGCTGGAGAACGAGAGCCGGCCTGAGTCGAGCTTCAGCATGGACTCGGAGCTGGGCCGTGGCCGCGAGAACGGAGGTGGCGTGCCACCGGGGGTGGCGGGCGCA + +a score=424364.0 +s hg18.chr14 7657246 47 - 106368585 GCCggaggaggaggacgaggaggaggaggaggaggaggaggagCTGC +s panTro2.chr14 7806037 47 - 107349158 GCCggaggaggaggacgaggaggaggaggaggaggaggaggagCTGC +s mm8.chr12 12098878 44 - 120463159 GCCTgaggacga---cgaggacgaggaggaggaagaagaggagCTGC + +a score=0.0 +s hg18.chr14 7657213 33 - 106368585 CCACCACGAGAGCGACCCGTCGCTGGGCCACGA + +a score=1620466.0 +s hg18.chr14 7657080 133 - 106368585 TGAAGACGCACATGCACAAGGCCGGCTCGCTGGCCGGCCGCTCCGACGACGGGCTCTCGGCCGCCAGCTCCCCCGAGCCCGGCACCAGCGAGCTGGCGGGCGAGGGCCTCAAGGCGGCCGACGGTGACTTCCG +s panTro2.chr14 7805871 133 - 107349158 TGAAGACGCACATGCACAAGGCCGGCTCGCTGGCCGGCCGCTCCGACGACGGGCTCTCGGCCGCCAGCTCCCCCGAGCCCGGCACCAGCGAGCTGGCGGGCGAGGGCCTCAAGGCGGCCGACGGCGACTTCCG +s mm8.chr12 12098715 130 - 120463159 TGAAGACGCACATGCACAAGGCGGGCTCTCTGGCTGGCCGCTCAGACGACGGGCTCTCAGCTGCCAGCTCCCCTGAGCCGGGCACCAGCGAGCTGCCAGGTGA---CCTGAAAGCGGCCGATGGCGACTTCCG + +a score=1419683.0 +s hg18.chr14 7657003 77 - 106368585 TCACACGGGCGAGAAGCCCTACAAGTGCCAGCTGTGCGACCACGCGTGCTCGCAGGCCAGCAAGCTCAAGCGCCACA +s panTro2.chr14 7805794 77 - 107349158 TCACACGGGCGAGAAGCCCTACAAGTGCCAGCTGTGCGACCACGCGTGCTCGCAGGCCAGCAAGCTCAAGCGCCACA +s mm8.chr12 12098638 77 - 120463159 CCACACGGGCGAGAAGCCCTACAAGTGCCAGCTGTGCGACCATGCGTGCTCGCAGGCGAGCAAGCTCAAGCGCCACA + +a score=2586302.0 +s hg18.chr14 7656851 152 - 106368585 AGCCCCAAGTCCCCGTTCCTGAGCACGCCGCCGCTGCCGCCCATGCCCCCTGGCGGCACGCCGCCCCCGCAGCCGCCAGCCAAGAGCAAGTCGTGCGAGTTCTGCGGCAAGACCTTCAAGTTCCAGAGCAATCTCATCGTGCACCGGCGCAG +s panTro2.chr14 7805642 152 - 107349158 AGCCCCAAGTCCCCGTTCCTGAGCACGCCGCCGCTGCCGCCCATGCCCCCTGGCGGCACGCCGCCCCCGCAGCCGCCGGCCAAGAGCAAGTCGTGCGAGTTCTGCGGCAAGACCTTCAAGTTCCAGAGCAATCTCATCGTGCACCGGCGCAG +s mm8.chr12 12098489 149 - 120463159 AGTCCCAAGTCCCCGTTCCTCAGCACGCCACCGCTGCCACCCATGCCTGCGGGC---ACACCGCCACCGCAGCCGCCTGCCAAGAGCAAGTCCTGTGAGTTCTGCGGCAAGACCTTCAAGTTCCAGAGCAATCTCATCGTGCACCGGCGCAG + +a score=2626021.0 +s hg18.chr14 7656695 156 - 106368585 GACCGAGTCATGCGCCTGAACCCCATGGCCATCGACTCGCCCGCCATGGACTTCTCGCGGCGGCTCCGCGAGCTGGCGGGCAACAGCTCCACGCCGCCGCCCGTGTCCCCGGGCCGCGGCAACCCTATGCACCGGCTCCTGAACCCCTTCCAGCCC +s panTro2.chr14 7805486 156 - 107349158 GACCGAGTCATGCGCCTGAACCCCATGGCCATCGACTCGCCCGCCATGGACTTCTCGCGGCGGCTCCGCGAGCTGGCGGGCAACAGCTCCACGCCGCCGCCCGTGTCCCCGGGCCGCGGCAACCCTATGCACCGGCTCCTGAACCCCTTCCAGCCC +s mm8.chr12 12098333 156 - 120463159 GACCGAGTCATGCGCCTGAACCCCATGGCCATAGACTCTCCTGCCATGGACTTCTCCCGGCGGCTGCGAGAACTGGCCGGCAACAGCTCCACGCCGCCGCCCGTGTCCCCAGGCCGTGGCAACCCTATGCACCGGCTGCTGAACCCTTTCCAGCCC + +a score=2119797.0 +s hg18.chr14 7656589 106 - 106368585 GCCGGGCACGCCGCCTCTCTTCAGTCCCCCGCCGCGCCACCACCTGGACCCGCACCGCCTCAGTGCCGAGGAGATGGGGCTCGTCGCCCAGCACCCCAGTGCCTTC +s panTro2.chr14 7805380 106 - 107349158 GCCGGGCACGCCGCCTCTCTTCAGTCCCCCGCCGCGCCACCACCTGGACCCGCACCGCCTCAGTGCCGAGGAGATGGGGCTCGTCGCCCAGCACCCCAGTGCCTTC +s mm8.chr12 12098227 106 - 120463159 GCCAGGTACGCCACCGCTCTTCAGCCCACCGCCACGCCATCACTTGGACCCACACCGCCTCAGTGCAGAGGAGATGGGGCTCGTGGCCCAGCACCCCAGTGCCTTC + +a score=4942642.0 +s hg18.chr14 7656300 289 - 106368585 GTAAAGATGAGCCTTCCAGCTACATTTGCACAACATGCAAGCAGCCCTTCAACAGCGCGTGGTTCCTGCTGCAGCACGCGCAGAACACGCACGGCTTCCGCATCTACCTGGAGCCCGGGCCGGCCAGCAGCTCGCTCACGCCGCGGCTCACCATCCCGCCGCCGCTCGGGCCGGAGGCCGTGGCGCAGTCCCCGCTCATGAATTTCCTGGGCGACAGCAACCCCTTCAACCTGCTGCGCATGACGGGCCCCATCCTGCGGGACCACCCGGGCTTCGGCGAGGGCCGCCT +s panTro2.chr14 7805091 289 - 107349158 GTAAAGATGAGCCTTCCAGCTACATTTGCACAACATGCAAGCAGCCCTTCAACAGCGCGTGGTTCCTGCTGCAGCACGCGCAGAACACGCACGGCTTCCGCATCTACCTGGAGCCCGGGCCGGCCAGCAGCTCGCTCACGCCGCGGCTCACCATCCCGCCGCCGCTCGGGCCGGAGGCCGTGGCGCAGTCCCCGCTCATGAATTTCCTGGGCGACAGCAACCCCTTCAACCTGCTGCGCATGACGGGCCCCATCCTGCGGGACCACCCGGGCTTCGGCGAGGGCCGCCT +s mm8.chr12 12097938 289 - 120463159 GTAAAGATGAGCCTTCCAGCTACATTTGCACAACATGCAAGCAGCCCTTCAACAGCGCCTGGTTCCTGCTGCAGCACGCACAGAACACACATGGCTTCCGAATCTACCTGGAGCCTGGGCCGGCCAGCACCTCGCTCACGCCCAGGCTCACCATCCCGCCACCGCTCGGGCCGGAGACCGTGGCGCAGTCCCCACTCATGAATTTCCTGGGGGACAGCAATCCTTTCAACCTGCTGCGCATGACGGGCCCCATCCTGCGGGACCACCCTGGCTTCGGTGAGGGCCGCTT + +a score=629708.0 +s hg18.chr15 58852016 27 - 100338915 TATAAACACGATTATGTTTCTCACTAA +s mm8.chr2 61086875 27 - 181976762 TATAAACATGATTATGTTTCTCACTAA +s panTro2.chr15 59529448 27 - 100063422 TATAAACACGATTATGTTTCTCACTAA + +a score=373301.0 +s hg18.chr15 58851981 35 - 100338915 TTGGGGAGAGAATTGGATTCAAGCAGCATCCAAAA +s panTro2.chr15 59529413 35 - 100063422 TTGGGGAGAGAATTGGATTCAAGCAGCATCCAAAA +s mm8.chr2 61086840 35 - 181976762 TTGGGGAGAGAATTGGATTCAAGCAGCATCCAAAA + +a score=2237520.0 +s hg18.chr15 58851855 126 - 100338915 ATATTGCTTTAGGGGTATTTGATGTGGTGGTGACGGACCCCTCATGCCCAGCCTCGGTGCTGAAGTGTGCTGAAGCATTGCAGCTGCCTGTGGTGTCACAAGAGTGGGTGATCCAGTGCCTCATTG +s panTro2.chr15 59529287 126 - 100063422 ATATTGCTTTGGGGGTATTTGATGTGGTGGTGACGGACCCCTCATGCCCAGCCTCGGTGCTGAAGTGTGCTGAAGCATTGCAGCTGCCTGTGGTGTCACAAGAGTGGGTGATCCAGTGCCTCATTG +s mm8.chr2 61086714 126 - 181976762 ACATTGCTTTAGGGGTATTTGATGTGGTGGTGACAGACCCCTCATGCCCAGCCTCGGTGCTCAAGTGTGCTGAAGCCTTGCAACTGCCTGTGGTATCACAAGAATGGGTGATCCAGTGCCTCATTG + +a score=562984.0 +s hg18.chr15 41673708 75 + 100338915 ATGGCTGGTCCCTTCTCCCGTCTGCTGTCCGCCCGCCCGGGACTCAGGCTCCTGGCTTTGGCCGGAGCGGGGTCT +s panTro2.chr15 40727968 75 + 100063422 ATGGCTGGTCCCTTCTCCCGTCTGCTGTCCGCCCGCCCGGGACTCAGGCTCCTGGCTTTGGCCGGAGCGGGGTCT +i panTro2.chr15 C 0 C 0 +s mm8.chr2 121050290 75 + 181976762 ATGGCTGGTCCCTTCTCCCGTCTGCTGTCTGCCCGCCCTGGACTCAGGCTCCTGGCTTTGGCTGGAGCTGGGTCT +i mm8.chr2 C 0 C 0 + +a score=535926.0 +s hg18.chr15 41673783 74 + 100338915 CTAGCCGCTGGGTTTCTGCTCCGACCGGAACCTGTACGA---GCTGCCAGTGAACGACGGAGGCTGTATCCCCCGAG +s panTro2.chr15 40728043 74 + 100063422 CTAGCCGCTGGGTTTCTGCTCCGACCGGAACCTGTACGA---GCGGCCAGTGAACGACGGAGGCTGTATCCCCCGAG +i panTro2.chr15 C 0 C 0 +s mm8.chr2 121050365 77 + 181976762 CTCACCGCCGGGATTCTGCTCCGCCCGGAATCTGTAGGAGCTGCCGCTGCTGAACGGAGGAGACTGTATCCCCCGAG +i mm8.chr2 C 0 C 0 + +a score=1893961.0 +s hg18.chr15 58659665 89 - 100338915 GTCGAAGTACAGCCTGGGGCCTCCAGGACTGGTCACGACCTTCCTGGTCCCTGGTATTGACTATCAGCTTCCTTGGCCACCTGCTATGA +s panTro2.chr15 59329615 89 - 100063422 GTCGAAGTACAGCCTGGGGCCTCCAGGACTGGTCACGACCTTCCTGGTCCCTGGTATTGACTATCAGCTTCCTTGGCCACCTGCTATGA +s mm8.chr2 60921257 89 - 181976762 GTCGAAACTCAGCCTGGGGTCTCTACGACTGGTTCCAAGCCTCCTGGGCCCTGGCATTGCCCGTCAGCATTTTTGGCCACCTATTATGA + +a score=118616.0 +s hg18.chr15 41826029 31 + 100338915 ATGCGCCTCCGCCGCCTAGCGCTGTTCCCGG +s mm8.chr2 121105479 31 + 181976762 ATGCGCTTCAGCTGCCTAGCTCTGCTCCCGG +i mm8.chr2 C 0 C 0 +s panTro2.chr15 40866268 31 + 100063422 ATGCGCCTCCGCCGCCTAGCGCTGTTCCCGG +i panTro2.chr15 C 0 C 0 + +a score=284293.0 +s hg18.chr15 41826060 57 + 100338915 GTGTGGCGCTGCTTCTTGCCGCGGCCCGCCTCGCCGCTGCCTCCGACGTGCTAGAAC +s panTro2.chr15 40866299 57 + 100063422 GTGTGGCGCTGCTTCTTGCCGCGGCCCGCCTCGCCGCTGCCTCCGACGTGCTAGAAC +i panTro2.chr15 C 0 C 0 +s mm8.chr2 121105510 57 + 181976762 GCGTGGCGCTGCTGCTCGCCTCGGCCCGTCTCGCCGCCGCCTCCGATGTGTTGGAAC +i mm8.chr2 C 0 C 0 + +a score=259946.0 +s hg18.chr15 41826117 36 + 100338915 TCACGGACGACAACTTCGAGAGTCGCATCTCCGACA +s mm8.chr2 121105567 36 + 181976762 TGACGGACGAAAACTTCGAGAGTCGCGTCTCCGACA +i mm8.chr2 C 0 C 0 +s panTro2.chr15 40866356 36 + 100063422 TCACGGACGACAACTTCGAGAGTCGCATCTCCGACA +i panTro2.chr15 C 0 C 0 + +a score=478199.0 +s hg18.chr15 41826153 43 + 100338915 CGGGCTCTGCGGGCCTCATGCTCGTCGAGTTCTTCGCCCCCTG +s panTro2.chr15 40866392 43 + 100063422 CGGGCTCTGCGGGCCTCATGCTCGTCGAGTTCTTCGCCCCCTG +i panTro2.chr15 C 0 C 0 +s mm8.chr2 121105603 43 + 181976762 CGGGCTCGGCGGGGCTCATGCTAGTCGAGTTCTTCGCCCCCTG +i mm8.chr2 C 0 C 0 + +a score=71812.0 +s hg18.chr16 142908 17 + 88827254 ATGTCTCTGACCAAGAC +s mm8.chr11 32176663 17 + 121798632 ATGTCTCTGATGAAGAA +i mm8.chr11 C 0 C 0 +s panTro2.chr16 146323 17 + 90682376 ATGTCTCTGACCAAGAC +i panTro2.chr16 C 0 C 0 + +a score=320391.0 +s hg18.chr16 142925 78 + 88827254 TGAGAGGACCATCATTGTGTCCATGTGGGCCAAGATCTCCACGCAGGCCGACACCATCGGCACCGAGACTCTGGAGAG +s mm8.chr11 32176680 78 + 121798632 TGAGAGAGCTATCATCATGTCCATGTGGGAGAAGATGGCTGCTCAGGCCGAGCCCATTGGCACTGAGACTCTAGAGAG +i mm8.chr11 C 0 C 0 +s panTro2.chr16 146340 78 + 90682376 TGAGGGGACCATCATTGTGTCCATGTGGGCCAAGATCTCCACGCAGGCCGACACCATCGGCACCGAGACTCTGGAGAG +i panTro2.chr16 C 0 C 0 + +a score=1751098.0 +s hg18.chr16 88647174 117 - 88827254 CGGAAATTGTCCCGGTCCCGGTCCCGAGATAGACATCGGCGCCACCGCAGCCGTTCCCGGAGCCACAGCCGGGGACATCGTCGGGCTTCCCGGGACCGAAGTGCGAAATACAAGTAA +s panTro2.chr16 90501243 117 - 90682376 CGGAAATTGTCCCGGTCCCGGTCCCGAGATAGACATCGGCGCCACCGCAGCCGTTCCCGGAGCCACAGCCGGGGACATCGTCGGGCTTCCCGGGACCGGAGTGCGAAATACAAGTAA +s mm8.chr17 26007615 117 + 95177420 CGGAAGTTTTCCCGTTCCAGATCCCGAGATAGATACAGGCGCCATCGCAGCCGTTCCCGGAGCCACAGCCGGGGTCACCGCCGGGCTTCCAGGGACCGGAGTACAAAATACAAGTAA + +a score=362047.0 +s hg18.chr16 88647119 55 - 88827254 GTCACGCTCCCGGGATCGGCGTCGGAGGCGGTCAAGATCTACCTCCCGAGAGCGA +s panTro2.chr16 90501188 55 - 90682376 GTCACGCTCCCGGGATCGGCGTCGGAGGCGGTCAAGATCTACCTCCCGAGAGCGA +s mm8.chr17 26007560 55 + 95177420 GTCACGCTCCCGGGATCGTCGACGGAGGCGGTCTAGGTCTACCTCCAGAGAGCGG + +a score=119311.0 +s hg18.chr16 244413 4 + 88827254 ATGT +s panTro2.chr16 250030 4 + 90682376 ATGT +i panTro2.chr16 C 0 C 0 +s mm8.chr17 69229272 4 - 95177420 ATGA +i mm8.chr17 C 0 C 0 + +a score=805217.0 +s hg18.chr16 244417 122 + 88827254 TGGACCACAAGGACTTAGAGGCCGAAATCCACCCCTTGAAAAATGAAGAAAGAAAATCGCAGGAAAATCTGGGAAATCCATCAAAAAATGAGGATAACGTGAAAAGCGCGCCTCCACAGTCC +s panTro2.chr16 250034 122 + 90682376 TGGACCACAAGGACTTAGAAGCCGAAATCCACCCCTTGAAAAATGAAGAAAGAAAATCGCAGGAAAATCTGGGAAATCCATCAAAAAATGAGGATAACGTGAAAAGCGCGCCTCCACAGTCC +i panTro2.chr16 C 0 C 0 +s mm8.chr17 69229276 122 - 95177420 TGGACAACAAGGACTTAGAAGCTGAAATACACCCCTTGAAGAATGAGGACAAGAAATCACAGGAAAACCCAGGAAACCTACCAAGAAACGAAGATAACTTGAAGAGCAAGCCTGTGCCTTCC +i mm8.chr17 C 0 C 0 + +a score=459982.0 +s hg18.chr16 244539 41 + 88827254 CGGCTCTCCCGGTGCCGAGCGGCGGCGTTTTTTCTTTCATT +s panTro2.chr16 250156 41 + 90682376 CGGCTCTCCCGGTGCCGAGCGGCGGCGTTTTTTCTTTCATT +i panTro2.chr16 C 0 C 0 +s mm8.chr17 69229398 41 - 95177420 CGCTTGTCCCGGTGCCGCACAGTGGCATTTTTCCTTTCCCT +i mm8.chr17 C 0 C 0 + +a score=699262.0 +s hg18.chr16 244580 60 + 88827254 GTTTCTCTGCCTTTTTGTGGTGTTCGTCGTCTCATTCGTCATCCCGTGTCCAGACCGGCC +s panTro2.chr16 250197 60 + 90682376 GTTTCTCTGCCTTTTTGTGGTGTTCGTCGCCTCATTCGTCATCCCGTGTCCAGACCGGCC +i panTro2.chr16 C 0 C 0 +s mm8.chr17 69229439 60 - 95177420 GTTCACCTGCCTCTTCGTGGTGTTTGTCCTGTCTTTCATCATCCCATGTCCAGACCGTCC +i mm8.chr17 C 0 C 0 + +a score=263619.0 +s hg18.chr16 244640 41 + 88827254 GGCGTCACAGCGAATGTGGAGGATAGACTACAGTGCCGCTG +s panTro2.chr16 250257 41 + 90682376 GGCGTCACAGCAAATGTGGAGGATAGACTACAGTGCCGCTG +i panTro2.chr16 C 0 C 0 +s mm8.chr17 69229499 41 - 95177420 CTCCTCACAGGGCACGTGGAAGCTTGACTACAACAATGCAG +i mm8.chr17 C 0 C 0 + +a score=-184929.0 +s hg18.chr16 88567958 28 - 88827254 CCCTGGGGGTGGAGATGGGGTGGCCTAG +s panTro2.chr16 90415110 23 - 90682376 -----GGGGTGGAGATGGGGTGGCCTAG +s mm8.chr17 25938305 28 + 95177420 CCCTGAAGGTGCCGATGGGGAGTAGTAG + +a score=-142475.0 +s hg18.chr16 88567938 20 - 88827254 GAGCCCACAGCGGCTTGTGG +s mm8.chr17 25938285 20 + 95177420 GAGCCTGCAGCAACCAGTTC + +a score=-5251.0 +s hg18.chr16 88567925 13 - 88827254 TCCCACCCCTGTG +s mm8.chr17 25938272 13 + 95177420 GTCTACCCCCAGG + +a score=428688.0 +s hg18.chr16 88567871 54 - 88827254 CGTGTTCCCGTTTACGTGGAGGCCACGGCACTCGAGCCCCAGCCCTGCACTCCT +s panTro2.chr16 90414601 54 - 90682376 CGTGTTCCCAATTACGTGGAGGCCACGGCACTCGAGCCCCAGCCCTGCACTCCT +s mm8.chr17 25938218 54 + 95177420 GCCATTTCCATTCTTGCGGAAGCCTCTGCACTCAAGCCCCAGCCCTGCTCTCCA + +a score=1837801.0 +s hg18.chr18 52330965 74 - 76117153 ACTATGATTACCTGAACGACTGGGGGCCACGGTTCAAGAAACTTGCTGACATGTATGGTGGAGGTGATGACTGA +s panTro2.chr18 53421695 74 - 77261746 ACTATGATTACCTGAACGACTGGGGGCCACGGTTCAAGAAACTTGCTGACATGTATGGTGGAGGTGATGACTGA +s mm8.chr18 74003599 74 - 90736837 ACTATGACTACCTGAATGACTGGGGACCCCGCTTCAAGAAACTGGCGGACATGTACGGCGGTGGTGACGACTGA + +a score=469497.0 +s hg18.chr18 52330944 21 - 76117153 CAAGTAGTGGTGGTGAGCAGG +s panTro2.chr18 53421674 21 - 77261746 CAAGTAGTGGTGGTGAGCAGG +s mm8.chr18 74003578 21 - 90736837 CCAGTAGCGGTGGGGACCAGG + +a score=2266476.0 +s hg18.chr18 52330832 112 - 76117153 GGCCTTAAAGCGGCTGACAATGACCCCACAGCTCCACCATATGACTCCCTGTTAGTGTTTGACTATGAAGGCAGTGGCTCCACTGCTGGGTCCTTGAGCTCCCTTAATTCCT +s panTro2.chr18 53421562 112 - 77261746 GGCCTTAAAGCGGCTGACAATGACCCGACAGCTCCACCATATGACTCCCTGTTAGTGTTTGACTATGAAGGCAGTGGCTCCACTGCTGGGTCCTTGAGCTCCCTTAATTCCT +s mm8.chr18 74003466 112 - 90736837 GGCCTTAAAGCTGCTGACAACGACCCCACGGCGCCACCGTATGACTCCCTCTTAGTCTTTGACTACGAGGGCAGCGGCTCCACGGCTGGCTCCTTGAGCTCCCTCAACTCCT + +a score=1391235.0 +s hg18.chr18 59406881 165 + 76117153 ATGGATTCACTTGGCGCCGTCAGCACTCGACTTGGGTTTGATCTTTTCAAAGAGCTGAAGAAAACAAATGATGGCAACATCTTCTTTTCCCCTGTGGGCATCTTGACTGCAATTGGCATGGTCCTCCTGGGGACCCGAGGAGCCACCGCTTCCCAGTTGGAGGAG +s panTro2.chr18 60102164 165 + 77261746 ATGGATTCACTTGGCGCCGTCAGCACTCGACTTGGGTTTGATCTTTTCAAAGAGCTGAAGAAAACAAATGATGGCAACATCTTCTTTTCCCCTGTGGGCATCTTGACTGCAATTGGCATGCTCCTCCTGGGGACCCGAGGAGCCACCGCTTCCCAGTTGGAGGAG +i panTro2.chr18 C 0 C 0 +s mm8.chr1 108809701 165 + 197069962 ATGGACTCACTAGGCACAGCAGCCACACAGTTCCTGTTTGATCTTTTCAAAGAACTGAATAAAACAAATGATGGCAACGTCTTCTTTTCCCCTGTGGGCATCTCAACAGCCATTGGCATGATCATCCTGGGGACCCGAGGAGCCACTGCTTCTGAGTTACAGAAG +i mm8.chr1 C 0 C 0 + +a score=725586.0 +s hg18.chr18 16661111 110 - 76117153 CATCTCCTTCAACTAATGAAGAGTTCTGTTGTAATCACCCTTTCCTATTCTTCATAAGGCAAAATAAGACCAACAGCATCCTCTTCTATGGCAGATTCTCATCCCCATAG +s panTro2.chr18 17099295 110 - 77261746 CATCTCCTTCAACTAATGAAGAGTTCCGTTGTAATCACCCTTTCCTATTCTTCATAAGGCAAAATAAGACCAACAGCATCCTCTTCTATGGCAGATTCTCATCCCCGTAG +s mm8.chr1 88222178 101 - 197069962 TATCTTTACAGATTACAGAAGATTTCTATTGTGATCATCCATTG---------GTCAAGCACAGTAAGACCAACAGCATCCTCTTCTTTGGCACAATCTCTTCCCCTTAA + +a score=-126872.0 +s hg18.chr18 16661103 8 - 76117153 CGAATTAT +s panTro2.chr18 17099287 8 - 77261746 CGAATTAT +s mm8.chr1 88222173 5 - 197069962 TA---ATT + +a score=1725446.0 +s hg18.chr18 16660844 259 - 76117153 TGATGGAATGGACAAGTTTGCAGAATATGAGAGAGACATGTGTCGATTTACACTTACCTCGGTTCAAAATGGAAGAGAGCTATGACCTCAAGGACACGTTGAGAACCATGGGAATGGTGAATATCTTCAATG---GGGATGCAGACCTCTCAGGCATGACCTGGAGCCACGGTCTCTCAGTATCTAAAGTCCTACACAAGGCCTTTGTGGAGGTCACTGAGGAGGGAGTGGAAGCTGCAGCTGCCACCGCTGTAGTAGTAGT +s panTro2.chr18 17099028 259 - 77261746 TGATGGAATGGACAAGTTTGCAGAATATGAGAGAGACACATGTCGATTTACACTTACCTCGGTTCAAAATGGAAGAGAGCTATGACCTCAAGGACACGTTGAGAACCATGGGAATGGTGAATATCTTCAATG---GGGATGCAGACCTCTCAGGCATGACTGGGAGCCGCGGTCTCTCGGTATCTAAAGTCCTACACAAGGCCTTTGTGGAGGTCACTGAGGAGGGAGCGGAAGCTGCAGCTGCCACCGCTGTAGTAGTAGT +s mm8.chr1 88221911 262 - 197069962 TACTAGAATGGACAAGAGCAGAAAATATGCATATGACCGAGTTGTATTTATCTTTGCCTCGGTTCAAAGTGGAAGAGAAGTATGACCTCTCAGTTCCATTGAAACACATGGGGATGGTTGGCGCCTTTGATCCACAGAAGGCTGACTTCTCTGGCATGAACAGCACTCAAGGTCTTGTGGTGTCTAAAGTTTTACACAAGTCCTTTGTGGAGGTAAATGAAGAGGGAACAGAAGCTGCTGCTACCACGGGGATAAAATCCCA + +a score=231361.0 +s hg18.chr18 16660816 28 - 76117153 CTTGAAGAGAAACTCACTGCTGAGAAAT +s panTro2.chr18 17099000 28 - 77261746 CTTGAAGAGAAACTCACTGCTGAGAAAT +s mm8.chr1 88221883 28 - 197069962 CTTGAAGAACAACTCTCTACTGAAAAGT + +a score=2290170.0 +s hg18.chr18 59600586 154 + 76117153 ATGGCCTCCCTTGCTGCAGCAAATGCAGAGTTTTGCTTCAACCTGTTCAGAGAGATGGATGACAATCAAGGAAATGGAAATGTGTTCTTTTCCTCTCTGAGCCTCTTCGCTGCCCTGGCCCTGGTCCGCTTGGGCGCTCAAGATGACTCCCTCT +s panTro2.chr18 60332677 154 + 77261746 ATGGCCTCCCTTGCTGCAGCAAATGCAGAGTTTTGCTTCAACCTGTTCAGAGAGATGGATGACAATCAAGGAAATGGAAATGTGTTCTTTTCCTCTCTGAGCCTCTTCGCTGCCCTGGCCCTGGTCCGCTTGGGCGCTCAAGATGACTCTCTCT +i panTro2.chr18 C 0 C 0 +s mm8.chr1 109255795 154 + 197069962 ATGGCCTCCCTTGCTGCAGCAAATGCAGAATTTGGCTTCGACTTATTCAGAGAGATGGATAGTAGCCAAGGAAATGGAAATGTATTCTTCTCTTCCCTGAGCATCTTCACTGCCCTGACCCTAATCCGTCTGGGTGCTCGAGGTGACTGTGCAC +i mm8.chr1 C 0 C 0 + +a score=17919.0 +s hg18.chr18 59600740 14 + 76117153 CTCAGATTGATAAG +s panTro2.chr18 60332831 14 + 77261746 CTCAGATTGATAAG +i panTro2.chr18 C 0 C 0 +s mm8.chr1 109255949 14 + 197069962 GTCAGATTGACAAG +i mm8.chr1 C 0 C 0 + +a score=177042.0 +s hg18.chr19 59068595 42 + 63811651 ATGCCAGTGACGGTAACCCGCACCACCATCACAACCACCACG +s panTro2.chr19 59561975 42 + 64473437 ATGCCAGTGACGGTAACCCGCACCACCATCACAACCACCACG +i panTro2.chr19 C 0 C 0 +s mm8.chr7_random 82256 42 - 243910 ATGCCGGTAACAGTAACTCGTACAACCATCACGACTACAACG +i mm8.chr7_random C 0 C 0 + +a score=-114935.0 +s hg18.chr19 59068637 25 + 63811651 ACGTCATCTTCGGGCCTGGGGTCCC +s panTro2.chr19 59562017 25 + 64473437 ACGTCATCTTCGGGCCTGGGGTCCC +i panTro2.chr19 C 0 C 0 +s mm8.chr7_random 82298 7 - 243910 TCA------------------TCCT +i mm8.chr7_random C 0 C 0 + +a score=340234.0 +s hg18.chr19 59068662 63 + 63811651 CCATGATCGTGGGGTCCCCTCGGGCCCTGACACAGCCCCTGGGTCTCCTTCGCCTGCTGCAGC +s mm8.chr7_random 82305 63 - 243910 CCACCACTGTGGGGTCCGCTCGGGCGCTGACCCAGCCGCTGGGCCTCCTCCGCCTCCTGCAGC +i mm8.chr7_random C 0 C 0 +s panTro2.chr19 59562042 63 + 64473437 CCACGATCGTGGGGTCCCCTCGGGCCCTGACACAGCCCCTGGGTCTCCTTCGCCTGCTGCAGC +i panTro2.chr19 C 0 C 0 + +a score=295172.0 +s hg18.chr19 59068725 23 + 63811651 TGGTGTCTACCTGCGTGGCCTTC +s mm8.chr7_random 82368 23 - 243910 TAATATCCACCTGTGTGGCTTTC +i mm8.chr7_random C 0 C 0 +s panTro2.chr19 59562105 23 + 64473437 TGGTGTCTACCTGCGTGGCCTTC +i panTro2.chr19 C 0 C 0 + +a score=161030.0 +s hg18.chr19 59068748 38 + 63811651 TCGCTGGTGGCTAGCGTGGGCGCCTGGACGGGGTCCAT +s panTro2.chr19 59562128 38 + 64473437 TCGCTGGTGGCTAGCGTGGACGCCTGGACGGGGTCCAT +i panTro2.chr19 C 0 C 0 +s mm8.chr7_random 82391 38 - 243910 TCGCTGGTGGCCAGTGTGGGTGCCTGGACAGGGCCCAT +i mm8.chr7_random C 0 C 0 + +a score=1769153.0 +s hg18.chr19 59068786 173 + 63811651 GGGCAACTGGTCCATGTTCACCTGGTGCTTCTGCTTCTCCGTGACCCTGATCATCCTCATCGTGGAGCTGTGCGGGCTCCAGGCCCGCTTCCCCCTGTCTTGGCGCAACTTCCCCATCACCTTCGCCTGCTATGCGGCCCTCTTCTGCCTCTCGGCCTCCATCATCTACCCCA +s panTro2.chr19 59562166 173 + 64473437 GGGCAACTGGTCCATGTTCACCTGGTGCTTCTGCTTCTCCGTGACCCTGATCATCCTCATCGTGGAGCTGTGCGGGCTCCAGGCCCGCTTCCCCCTGTCTTGGCGCAACTTCCCCATCACCTTCGCCTGCTACGCGGCCCTCTTCTGCCTCTCGGCCTCCATCATCTACCCCA +i panTro2.chr19 C 0 C 0 +s mm8.chr7_random 82429 173 - 243910 GGGTAACTGGGCCATGTTCACCTGGTGTTTCTGCTTTGCTGTTACCCTCATCATCCTGATTGTGGAGTTAGGTGGACTCCAGGCCCACTTCCCCCTGTCATGGCGAAACTTCCCCATCACCTTTGCCTGCTACGCGGCCCTCTTCTGCCTGTCGTCTTCCATCATCTATCCCA +i mm8.chr7_random C 0 C 0 + +a score=1066893.0 +s hg18.chr19 59068959 145 + 63811651 CCACCTATGTCCAGTTCCTGTCCCACGGCCGTTCGCGGGACCACGCCATCGCCGCCACCTTCTTCTCCTGCATCGCGTGTGTGGCTTACGCCACCGAAGTGGCCTGGACCCGGGCCCGGCCCGGCGAGATCACTGGCTATATGGC +s panTro2.chr19 59562339 145 + 64473437 CCACCTATGTCCAGTTCCTGCCCCACGGTCGTTCGCGGGACCACGCCATCGCCGCCACCTTCTTCTCCTGCATCGCGTGTGTGGCTTACGCCACCGAAGTGGCCTGGACCCGGGCCCGGCCCGGCGAGATCACTGGCTATATGGC +i panTro2.chr19 C 0 C 0 +s mm8.chr7_random 82602 145 - 243910 CCACCTATGTGCAGTTCCTAGCTCATGGACGTACCCGGGACCATGCCATCGCTGCCACCACTTTCTCCTGCGTTGCCTGTTTGGCGTATGCCACTGAAGTGGCCTGGACCCGTGCAAGGCCCGGTGAGATCACTGGCTATATGGC +i mm8.chr7_random C 0 C 0 + +a score=925227.0 +s hg18.chr19 59069104 98 + 63811651 CACCGTACCCGGGCTGCTGAAGGTGCTGGAGACCTTCGTTGCCTGCATCATCTTCGCGTTCATCAGCGACCCCAACCTGTACCAGCACCAGCCGGCCC +s panTro2.chr19 59562484 98 + 64473437 CACCGTACCCGGGCTGCTGAAGGTGCTGGAGACCTTCGTGGCCTGCATCATCTTCGCGTTCATCAGCGACCCCAACCTGTACCAGCACCAGCCGGCCC +i panTro2.chr19 C 0 C 0 +s mm8.chr7_random 82747 98 - 243910 TACCGTGCCAGGGCTGCTCAAAGTTTTTGAGACCTTCGTAGCCTGTATCATCTTTGCCTTCATCAGTGAGCCGCTCCTGTATAATCAGAAGCCAGCCC +i mm8.chr7_random C 0 C 0 + +a score=900583.0 +s hg18.chr19 59069202 89 + 63811651 TGGAGTGGTGCGTGGCGGTGTACGCCATCTGCTTCATCCTAGCGGCCATCGCCATCCTGCTGAACCTGGGGGAGTGCACCAACGTGCTA +s panTro2.chr19 59562582 89 + 64473437 TGGAGTGGTGCGTGGCGGTGTACGCCATCTGCTTCATCCTAGCGGCCATCGCCATCCTGCTGAACCTGGGGGAGTGCACCAACGTGCTA +i panTro2.chr19 C 0 C 0 +s mm8.chr7_random 82845 89 - 243910 TGGAGTGGTGTGTGGCAGTCTATGCCATCTGCTTCATACTAGCAGGGGTGACCATCCTGCTCAACCTGGGGGATTGTACCAACGTGTTG +i mm8.chr7_random C 0 C 0 + +a score=962595.0 +s hg18.chr19 59069291 193 + 63811651 CCCATCCCCTTCCCCAGCTTCCTGTCGGGGCTGGCCTTGCTGTCTGTCCTCCTCTATGCCACCGCCCTTGTTCTCTGGCCCCTCTACCAGTTCGATGAGAAGTATGGCGGCCAGCCTCGGCGCTCGAGAGATGTAAGCTGCAGCCG------CAGCCATG------CCTACTACGTGTGTGCCTGGGACCGCCGACTGGCTGTGG +s panTro2.chr19 59562671 193 + 64473437 CCCATCCCCTTCCCCAGCTTCCTGTCGGGGCTGGCCTTGCTGTCTGTCCTCCTCTATGCCACTGCCCTTGTTCTCTGGCCCCTCTACCAGTTCGATGAGAAGTATGGCGGCCAGCCTCGGCGCTCGAGAGATGTAAGCTGCAGCCG------CAGCCATG------CCTACTACGTGTGTGCCTGGGACCGCCGACTGGCTGTGG +i panTro2.chr19 C 0 C 0 +s mm8.chr7_random 82934 205 - 243910 CCCATCCCTTTCCCCACCTTCCTCTCAGGCTTGGCCTTACTCTCTGTTCTCTTTTACGCCACTGCCATCGTCCTCTGGCCCCTCTACCAATTTGATCAGAGATATCAGGGCCAACCCCGCCGTTCAATGGATCCAAGCTGCACTCGTAGTATTAGTTATATACAACCCAACACGGTGTGTTTCTGGGACCGACGACTGGCGGTGT +i mm8.chr7_random C 0 C 0 + +a score=613379.0 +s hg18.chr19 59069484 80 + 63811651 CCATCCTGACGGCCATCAACCTACTGGCGTATGTGGCTGACCTGGTGCACTCTGCCCACCTGGTTTTTGTCAAGGTCTAA +s panTro2.chr19 59562864 80 + 64473437 CCATCCTGACGGCCATCAACCTACTGGCGTATGTGGCTGACCTGGTGCACTCTGCCCACCTGGTTTTTGTCAAGGTCTAA +i panTro2.chr19 C 0 C 0 +s mm8.chr7_random 83139 80 - 243910 CCATCCTGACAGGTATCAACCTGCTGGCATATGTGTCTGATCTGGTGTACTCCACTCGTCTGGTGTTCGTCAAGGTCTGA +i mm8.chr7_random C 0 C 0 + +a score=200956.0 +s hg18.chr19 4575513 112 - 63811651 CCCCCAAGGAGTGACCTATGCTGAGCTAAGCACCAGCGCCCTGTCTGAGGCAGCTTCAGACACCACCCAGGAGCCCCCAGGATCTCATGAATATGCGGCACTGAAAGTGTAG +s panTro2.chr19 4741219 112 - 64473437 CCCCCAAGGAGTGACCTATGCTGAGCTAAGCACCAGCGCCCTGTCTGAGGCAGCTTCAGACACCACCCAGGAGCCCCCAGGATCTCGTGAATATGCGGCACTGAAAGTGTAG + +a score=102826.0 +s hg18.chr19 4575505 8 - 63811651 ACGGCAGA +s panTro2.chr19 4741211 8 - 64473437 ACGGCAGA + +a score=177230.0 +s hg18.chr19 59297998 10 + 63811651 ATGGCTGCGA +s panTro2.chr19 59803934 10 + 64473437 ATGGCTGCGA +i panTro2.chr19 C 0 N 0 +s mm8.chr7 3220484 10 + 145134094 ATGGCCGGGA +i mm8.chr7 C 0 C 0 + +a score=406760.0 +s hg18.chr19 4509426 57 - 63811651 CGGGGTCCAGACAAACTGCTGCCCTACCCGACCCTGGCCAGCCCAGCCTCTGACTGA +s panTro2.chr19 4667557 57 - 64473437 CGGGGTCCAGACAAACTGCTGCCCTACCCGACCCTGGCCAGCCCAGCCTCTGACTGA +s mm8.chr7 141910596 57 - 145134094 CGAGAGCCAGACAAATTGCTACCCTACCCTACCCTGGCCAGCCCACCCTTTGACTAA + +a score=455500.0 +s hg18.chr19 4509363 63 - 63811651 ATTAAGGTTGAGGAAGACTTTGGCTTTGAAGCAGATGAGGCCCTGGATTCCAGTTGGGTTTCT +s panTro2.chr19 4667494 63 - 64473437 ATTAAGGTTGAGGAAGACTTTGGCTTTGAAGCAGATGAGGCCCTGGATTCCAGTTGGGTTTCT +s mm8.chr7 141910533 63 - 145134094 ATTAAGGTTGAGGAAGACTTTGGCTTTGAAGCAGATGAGGCCTTGGATTCAAGTTGGGTTTCC + +a score=-197707.0 +s hg18.chr2 118288583 6 + 242951149 GTCTCG +s mm8.chr1 73674351 6 - 197069962 GAGTCG +i mm8.chr1 I 86 C 0 +s panTro2.chr2b 118424760 6 + 248603653 GTCTCG +i panTro2.chr2b I 7 C 0 + +a score=207197.0 +s hg18.chr2 118288589 79 + 242951149 CTTCCACTTCTCCAGGGGGCGCTGCAAAGATTTTGGTCGCCAAAGATATCACGGTGCGCGCGTCTGGAAGCATTTCCGC +s panTro2.chr2b 118424766 79 + 248603653 CTTCCACTTCTCCAGGGGGCGCTGCAAAGATTTTGGTCGCCAAAGGTATCACGGTGCGCGCGTCTGGAAGCATTTCCGC +i panTro2.chr2b C 0 C 0 +s mm8.chr1 73674357 77 - 197069962 TCCTCCAGTCGCCAGGGGGCGCTGCAGGAAATTCGGTCTCCAAAGGGAACCCAGCTCTCA--CCAGGAACTGTTTCCGC +i mm8.chr1 C 0 C 0 + +a score=1362965.0 +s hg18.chr2 124556947 54 - 242951149 ACA-------GTAAACAC-GTGG----CTTGGATAACACCCATCATCCTATGAAGAATATAGGGAG +s panTro2.chr2b 130071925 54 - 248603653 ACA-------GTAAACAC-GTGG----CTTGGATAACACCCATCATCCTATGAAGAATATGGGGAG +s mm8.chr1 123328978 54 + 197069962 AGCCCTACAAA---GAACCGTGGGCAGTGTGGATGACACTCAGAGCCC---------CATAGGCAG + +a score=44574.0 +s hg18.chr2 220190202 12 + 242951149 atggcttaagct +s panTro2.chr2b 225564868 12 + 248603653 atggcttaagct +i panTro2.chr2b C 0 C 0 + +a score=189610.0 +s hg18.chr2 220190214 28 + 242951149 aattcgaagcaagtatgagccaccaaga +s panTro2.chr2b 225564880 28 + 248603653 aattcgaagcaagtatgagccaccaaga +i panTro2.chr2b C 0 C 0 + +a score=129775.0 +s hg18.chr2 22721476 64 - 242951149 aagaaactgccaaactgttttccagagtggttgtcccattttacctttccactggtaatgtatg +s panTro2.chr2b 22992739 64 - 248603653 aagaaactgccaaactgttttccagagtggttgtcccattttacctttccactggtaatgtatg + +a score=208210.0 +s hg18.chr2 22721289 187 - 242951149 atcactgcaccattcaccattcacccattaaaggacatctgcattgtctcagtttttggctattgcaaataaaactgctataaacatttgtttagtttattgtgtgaatataagtcttcctttctttgtgataaatgcccaagagtgcaattgctgagtcatatggtagttgtatgtttaggttttt +s panTro2.chr2b 22992552 187 - 248603653 atcactgcaccattaaccattcacccattaaaggacatctgcattgtctcagtttttggctattgcaaataaaactgctataaacatttgtttagtttattgtgtgaatataagtcttcctttctttgtgataaatgcccaagagtgcaattgctgcgtcatatggtagttgtatgtttaggttttt + +a score=27396.0 +s hg18.chr2 22721263 26 - 242951149 ttgtgtgcgtcaaaagcttattcttt +s panTro2.chr2b 22992526 26 - 248603653 ttgtttgcgtcaaaagcttattcttt + +a score=336518.0 +s hg18.chr2 22721013 250 - 242951149 Tagtgtcacaaccaaaatattgacatggacggggcaaaattagagaacatttcaatcacaataatggtcccccaagttgcctttttgtagctgtcccctccctaacctctggaaaccactaacccgttctctatttctgcaacactgtcactgtaagaatattgtataaatggaatcatacattgtgtagccttttgagaatggctttttcaactcagtgctattctctggagatacacagtttactgtg +s panTro2.chr2b 22992276 250 - 248603653 Tagtgtcacaaccaaaatattgacatggacggggcaaaattaaagaacatttcaatcacaataatggtcccccaagttgcctttttatagctgtcccctccctaacctctggaaaccactaacccgttctctatttctgcaacactgtcactgtaagaatattgtataaatggaatcatacattgtgtagccttttgagaatggctttttcaactcaatgctattctctggagatacacagtttaccgtg + +a score=86437.0 +s hg18.chr2 22720918 95 - 242951149 tttgagtgtttagtacctttatttttaatataatgtatttacctgtgtttgaatataatgtatttattttttaattatACATTTTATTTTAAGAT +s panTro2.chr2b 22992181 95 - 248603653 tttgagtgtttagtacctttatttttaatataatgtatttacctgtgtttgaatataatgtatttattttttaattatACATTTTATTTTAAGAT + +a score=271443.0 +s hg18.chr2 22720728 190 - 242951149 tctggtgtaaatactcccacaatggccaatttcaaactattagtgtgacatcactgaatgcagaattgggaagaaatgtgccatagcacatcactatagaatatttccaccatacagatataacagacataaataacttccagaatatagacaatagtaaaagtaacaaaataattgggaagtcatgaat +s panTro2.chr2b 22991991 190 - 248603653 tctggtgtaaatactcccacgatggccaatttcaagctattagtgtgacatcactgaatgcagaattgggaagaaatgtgccatagcacatcactatagaatatttccaccatacagatataacagacataaataacttccagaatatagacaatagtaaaagtaacaaaataattgggaagtcatgaat + +a score=197745.0 +s hg18.chr2 22720624 104 - 242951149 ATGCATGAGAAATTCCCTAAC---TTAAAAGCAgt-----cccggtaaaagtttaacaaccatctacgaaaaaaaggaggggaggacctaatttgtagtgtctgctgatttc +s panTro2.chr2b 22991887 104 - 248603653 atgcatgagaaattccctacc---ttaAAAGCAgt-----cccggtaaaagtttaacaaccatctacgaaaaaaaggaggggaggacctaatttgtagtgtctgctgatttc +s mm8.chr1 121613757 108 - 197069962 ATGC-TGTGGAA--CCCTCCTAGGTTGCGGACAGTGGAATGCTGGCAGACACAGAGCAGCCTGTTACGGAGAGGAAAGGGACACCATCTGCTT-GCATTGTCTGCTCATTTC + +a score=50206.0 +s hg18.chr2 22720593 31 - 242951149 TG----GAGTCATCCAGCATCTAAACCCACTTCCT +s panTro2.chr2b 22991856 31 - 248603653 TG----GAgtcatccagtatctaaacccacttcct +s mm8.chr1 121613722 35 - 197069962 CAGCCAGGGTTGGTCGGTACCTAAATGCACTTCTT + +a score=50867.0 +s hg18.chr2 22720539 54 - 242951149 ATAACTGATCTGAGACATTAT-CCATTTTTTGATTGACATTTGCTATTTGGGAGG +s panTro2.chr2b 22991802 54 - 248603653 ATAACTGATCTGAGACATTAT-CCATTTTTTGATTGACATTTGCTATTTGGGAGG +s mm8.chr1 121613670 52 - 197069962 A--A-TGATCTGAGGCCTTTCCCGACTTTTTAGTAAACATTCATTATTTGGGAAG + +a score=357793.0 +s hg18.chr2 22720367 172 - 242951149 ACC---ATCCTGCCATCTCTATGCTGGATATTAAAGAAATGAGATTATAAACAGCCAG-------GATTCCATTCCTCCA-----GCATCTGCTTCAACCACAGTCCACAACAGCCTTTTATAAAATGAGGGAAGCAATGAGGTAGAGAGGAAATAGCCTTAGGAAGAGCC-AGCTTCTTCCTCCTCT +s panTro2.chr2b 22991630 172 - 248603653 ACC---ATCCTGCCATCTCTATGCTGGATATTAAAGAAATGAGATTATAAACAGCCAG-------GATTCCATTCCTCCA-----GCATCTGCTTCAACCACAGTCCACAACAGCCTTTTATAAAATGAGGGAAGCAATGAGGTAGAGAGGAAATAGCCTTAGGAAGAGCC-AGCTTCTTCCTCCTCT +s mm8.chr1 121613496 173 - 197069962 ---aCTCTCATCCCATTCCTTTGCCAAAAATTCAAAAGATGAGATTACAAAAGATGAGAGGATGCAGTGCTCCAGACCCATCCTCAATTCCACCTCAACCACAGGCTGCAGGCCCCTTGAATAAAATAA----------AACACAGGGGG--GAAAGCCTGAGGAAGAGCCCAGGTTCTGTCTCCTCT + +a score=3197.0 +s hg18.chr2 22720323 44 - 242951149 AAAGAGATCTGAGCATTCATAAAACTCCATTTTTTTGTAGTTTT +s panTro2.chr2b 22991586 44 - 248603653 AAAGAGATCTGAGCATTCATAAAACTCCATTTTTTTGTAGTTTT +s mm8.chr1 121613132 41 - 197069962 --AAACAGCTTAGCATCCATAAGCCTCCATATTTTTGTAGCCT- + +a score=51138.0 +s hg18.chr2 22720280 43 - 242951149 GAT--GGAGAAAGATTAGAAACAGCAGTGCCTAGGGAA-AAGTGTA +s panTro2.chr2b 22991543 43 - 248603653 GAT--GGAGAAAGATTAGAAACGGCAGTGCCTAGGGAA-AAGTGTA +s mm8.chr1 121613086 46 - 197069962 AATGGACAGGGGGAATACAAAGGGCATTGACTAAGGGGGAAAGGTC + +a score=1119822.0 +s hg18.chr20 29105541 10 - 62435964 CCTCACCTGA +s panTro2.chr20 29927599 10 - 62293572 CCTCACCTGA +s mm8.chr2 26465210 10 - 181976762 CCTCACATGA + +a score=577225.0 +s hg18.chr20 33513606 69 + 62435964 ATGGAGACAAGAAGCCCTGGGTTGAACAACATGAAGCCCCAGTCACTGCAGCTGGTACTGGAAGAGCAG +s mm8.chr2 155653412 66 + 181976762 ATGGAGACAGGGAGCCCCGGGTTG---AACATGAAGCCCCAGTCCTTGCAGCTGGTGCTGGAGGGGCAG +i mm8.chr2 C 0 C 0 +s panTro2.chr20 32554547 69 + 62293572 ATGGAGACAAGAAGCCCTGGGTTGAACAACATGAAGCCCCAGTCACTGCAGCTGGTACTGGAAGAGCAG +i panTro2.chr20 C 0 C 0 + +a score=1499195.0 +s hg18.chr20 33513675 117 + 62435964 GTGCTGGCACTACAGCAGCAGATGGCAGAGAATCAGGCAGCCTCCTGGCGGAAGCTGAAGAACTCCCAGGAGGCCCAGCAGAGACAAGCAACCCTTGTGAGGAAGCTGCAGGCCAAG +s panTro2.chr20 32554616 117 + 62293572 GTGCTGGCACTACAGCAGCAGATGGCAGAGAATCAGGCAGCCTCCTGGCGGAAGCTGAAGAACTCCCAGGAGGCCCAGCAGAGACAAGCAACCCTTGTGAGGAAGCTGCAGGCCAAG +i panTro2.chr20 C 0 C 0 +s mm8.chr2 155653478 117 + 181976762 GTGCTGGCGCTGCAGCAGCAGATGGCCGAGAATCAGGCTGCCTCCTGGCGGAAACTGAAGAACTCCCAAGAGGCCCAGAAGAGACAAGCAACCCTCGTGAGGAAGCTGCAGGCCAAG +i mm8.chr2 C 0 C 0 + +a score=366540.0 +s hg18.chr20 28856457 7 - 62435964 TCCCTAG +s panTro2.chr20 29670686 7 - 62293572 TCCCTAG +s mm8.chr2 26282855 7 - 181976762 TCCCTAG + +a score=182231.0 +s hg18.chr20 28856437 20 - 62435964 ATTTTGGAAGATGGTCTGGT +s panTro2.chr20 29670666 20 - 62293572 ATTTTGGAAGATGGTCTGGT +s mm8.chr2 26282835 20 - 181976762 ATTTTGGAAGATGGTCTGAT + +a score=1173268.0 +s hg18.chr20 33593260 60 + 62435964 ATGGAGGCGCTGGGGAAGCTGAAGCAGTTCGATGCCTACCCCAAGACTTTGGAGGACTTC +s panTro2.chr20 32635706 60 + 62293572 ATGGAGGCGCTGGGGAAGCTGAAGCAGTTCGATGCCTACCCCAAGACTTTGGAGGACTTC +i panTro2.chr20 C 0 C 0 +s mm8.chr2 155699581 60 + 181976762 ATGGAGGCGCTGGGGAAGCTGAAGCAGTTCGATGCCTACCCTAAGACTCTGGAGGACTTC +i mm8.chr2 C 0 C 0 + +a score=512129.0 +s hg18.chr20 33593320 28 + 62435964 CGGGTCAAGACCTGCGGGGGCGCCACCG +s panTro2.chr20 32635766 28 + 62293572 CGGGTCAAGACCTGCGGGGGCGCCACCG +i panTro2.chr20 C 0 C 0 +s mm8.chr2 155699641 28 + 181976762 CGGGTCAAGACCTGCGGGGGTGCCACGG +i mm8.chr2 C 0 C 0 + +a score=610562.0 +s hg18.chr21 32707032 4 + 46944323 ATGC +s panTro2.chr21 32160918 4 + 46489110 ATGC +i panTro2.chr21 C 0 C 0 +s mm8.chr16 90720131 4 + 98252459 ATGC +i mm8.chr16 I 2 C 0 + +a score=749215.0 +s hg18.chr21 32707036 127 + 46944323 TTCTGCCGGGACGCGCACGCCAACCGCCGACGCCCCAGCCCGTGCAGCATCCCGGCCTCCGCCGGCAGGTAGAGCCGCCGGGGCAGCTCCTGCGCCTCTTCTACTGCACTGTCCTGGTCTGCTCCAA +s panTro2.chr21 32160922 127 + 46489110 TTCTGCCGGGACCCGCACGCCAACCGCCGACGCCCCAGCCCGTGCAGCATCCCGGCCTCCGCCGGCAGGTAGAGCCGCCGGGGCAGCTCCTGCGCCTCTTCTACTGCACTGTCCTGGTCTGCTCCAA +i panTro2.chr21 C 0 C 0 +s mm8.chr16 90720135 127 + 98252459 TCCTGCCAGGACACCCGCGTCCACCACCCGCGCCCCAATCGGCGCAGAATCAGGGCCTCCGCAGGCAGGTAGAGCCTCCGGGGCAGCTTCTGCGCCTGTTCTACTGCACGGTCCTAGTGTGCTCCAA +i mm8.chr16 C 0 C 0 + +a score=211993.0 +s hg18.chr21 32707163 29 + 46944323 AGAGATCTCAGCGCTCACCGACTTCTCTG +s panTro2.chr21 32161049 29 + 46489110 AGAGATCTCAGCGCTCACCGACTTCTCTG +i panTro2.chr21 C 0 C 0 +s mm8.chr16 90720262 29 + 98252459 AGAGACCTCCGCGCTCACCGATTTCTCTG +i mm8.chr16 C 0 C 0 + +a score=98928.0 +s hg18.chr21 14074369 313 - 46944323 TGGGTGCTTCCTGCATTGCGGGTCTCACGGGGAGGAGACGAGAGTGCCCCTGGTTGAGTCAGGAAAGAATTCTATCTTCACGTCGCTGCCAGCAAATGACCACAGCAGCTTCACGACCTCTGCAGGAACCTATCTTGGTAAAGAAACGGGGCCTATGTGGTGGCCGAGCCTCAGGTGTGGCCGAGCTTCAGGTGTGGCCCTTATGCACAGCACAGCCCAAGCCTGTGGGCACCACTCGCCCTGGGCTGCCTGGCACCTGGACTCCTTCCCATCCTTGGCCGAGGTCTGCGTGGCCCTTCAGGGCCGAATCTGA +s panTro2.chr21 14164701 313 - 46489110 TGGGTGCTTCCTGCATTGCGGGTCTCACGGGGAGGAGCCAAGAGTGCCCCTGGTTGAGTCAGGAAAGAATTCTATCTTCACGTCGCTGCCAGCAAATGACCACAGCAGCTTCACGACCTCTGCAGGAACCTATCTCGGTAAAGAAACAGAGCCTATCTGGTGGCTGAGCCTCAGGTGTGGCCGAGCTTCAGGTGTGGCCCTTATGCACAGCACAGCCCAAGCCTGTGGGCACCACTCGCCCTGGGCTGCCTGGCACCTGGACTCCTTCCCATCCTTGGCCGAGGTCTGCGTAGCCCTTCAGGGCCGAATCTGA + +a score=108541.0 +s hg18.chr21 14074301 68 - 46944323 ATGGAGCGCCCTCTCATCTGGCACCTTCCTGGCCTCTTTCCCAGGCCCCAGTTCTGTCCATGCAGCTG +s panTro2.chr21 14164633 68 - 46489110 ATGGAGCGCCCTCTCATCTGGCACCTGCCTGGCCTCTTTCCCAAGCCCCAGTTCTGTCCATGCAGCTG + +a score=637432.0 +s hg18.chr21 33321040 72 + 46944323 ATGGACTCGGACGCCAGCCTGGTGTCCAGCCGCCCGTCGTCGCCAGAGCCCGATGACCTTTTTCTGCCGGCC +s panTro2.chr21 32770081 72 + 46489110 ATGGACTCGGACGCCAGCCTGGTGTCCAGCCGCCCGTCGTCGCCAGAGCCCGATGACCTTTTTCTGCCGGCC +i panTro2.chr21 C 0 C 0 +s mm8.chr16 91115258 72 + 98252459 ATGGACTCGGACGCCAGCCTGGTGTCTAGTCGCCCATCGTCCCCAGAACCCGATGATCTTTTTCTGCCCGCC +i mm8.chr16 C 0 C 0 + +a score=158069.0 +s hg18.chr21 33321112 116 + 46944323 CGGAGTAAGGGCAGCAGCGGCAGCGCCTTCACTGGGGGCACCGTGTCCTCGTCCACCCCGAGTGACTGCCCGCCGGAGCTGAGCGCCGAGCTGCGCGGCGCTATGGGCTCTGCGGG +s panTro2.chr21 32770153 116 + 46489110 CGGAGTAAGGGCAGCAGCGGCAGCGCCTTCACTGGGGGCACCGTGTCCTCGTCCACCCCGAGCGACTGCCCGCCGGAGCTGAGCGCCGAGCTGCGCGGCGCTATGGGCTCTGCGGG +i panTro2.chr21 C 0 C 0 +s mm8.chr16 91115330 116 + 98252459 CGGAGCAAGGGGGGAAGCAGCAGCGGCTTCACAGGAGGGACTGTGTCCTCGTCCACGCCGAGCGACTGCCCGCCAGAGCTGAGCTCCGAGCTACGAGGGGCCATGGGCGCGTCAGG +i mm8.chr16 C 0 C 0 + +a score=56737.0 +s hg18.chr21 33321228 102 + 46944323 CGCGCATCCTGGGGACAAGCTAGGAGGCAGTGGCTTCAAGTCATCCTCGTCCAGCACCTCGTCGTCTACGTCGTCGGCGGCTGCGTCGTCCACCAAGAAGGA +s panTro2.chr21 32770269 102 + 46489110 CGCCCATCCTGGGGACAAGCTAGGAGGCAGTGGCTTCAAGTCATCCTCGTCCAGCACCTCGTCGTCTACGTCGTCGGCGGCTGCGTCGTCCACCAAGAAGGA +i panTro2.chr21 C 0 C 0 +s mm8.chr16 91115446 102 + 98252459 CGCGCATCCCGGGGACAAACTGGGCGGCGGTGGCTTCAAGTCATCTTCCTCCAGCACCTCCTCGTCCACGTCCTCGGCGGCCACGTCTTCCACCAAGAAAGA +i mm8.chr16 C 0 C 0 + +a score=1401662.0 +s hg18.chr21 33321330 142 + 46944323 CAAGAAGCAAATGACAGAGCCGGAGCTGCAGCAGCTGCGTCTCAAGATCAACAGCCGCGAGCGCAAGCGCATGCACGACCTCAACATCGCCATGGATGGCCTCCGCGAGGTCATGCCGTACGCACACGGCCCTTCGGTGCGC +s panTro2.chr21 32770371 142 + 46489110 CAAGAAGCAAATGACAGAGCCGGAGCTGCAGCAGCTGCGTCTCAAGATCAACAGCCGCGAGCGCAAGCGCATGCACGACCTCAACATCGCCATGGATGGCCTGCGCGAGGTCATGCCGTACGCACACGGCCCTTCGGTGCGC +i panTro2.chr21 C 0 C 0 +s mm8.chr16 91115548 142 + 98252459 CAAGAAGCAGATGACTGAGCCCGAGCTGCAGCAGCTGCGCCTGAAGATCAACAGCCGCGAACGCAAGCGCATGCACGACCTCAACATCGCCATGGACGGCCTGCGGGAGGTCATGCCTTACGCGCACGGGCCGTCGGTGCGC +i mm8.chr16 C 0 C 0 + +a score=494453.0 +s hg18.chr21 33321472 43 + 46944323 AAGCTTTCCAAGATCGCCACGCTGCTGCTGGCGCGCAACTACA +s panTro2.chr21 32770513 43 + 46489110 AAGCTTTCCAAGATCGCCACGCTGCTGCTGGCGCGCAACTACA +i panTro2.chr21 C 0 C 0 +s mm8.chr16 91115690 43 + 98252459 AAGCTCTCCAAGATCGCCACGCTGCTGCTGGCGCGAAACTACA +i mm8.chr16 C 0 C 0 + +a score=611248.0 +s hg18.chr21 33321515 47 + 46944323 TCCTCATGCTCACCAACTCGCTGGAGGAGATGAAGCGACTGGTGAGC +s panTro2.chr21 32770556 47 + 46489110 TCCTCATGCTCACCAACTCGCTGGAGGAGATGAAGCGACTGGTGAGC +i panTro2.chr21 C 0 C 0 +s mm8.chr16 91115733 47 + 98252459 TCCTCATGCTCACCAACTCGCTGGAGGAGATGAAGCGACTGGTGAGC +i mm8.chr16 C 0 C 0 + +a score=167373.0 +s hg18.chr21 33321562 184 + 46944323 GAGATCTACGGGGGCCACCACGCTGGCTTCCACCCGTCGGCCTGCGGCGGCCTGGCGCACTCCGCGCCCCTGCCCGCCGCCACCGCGCACCCGGCAGCAGCAGCGCACGCCGCACATCACCCCGCGGTGCACCACCCCATCctgccgcccgccgccgcagcggctgctgccgccgctgcagccg +s panTro2.chr21 32770603 184 + 46489110 GAGATCTACGGGGGCCACCACGCTGGCTTCCACCCGTCGGCCTGCGGCGGCCTGGCGCACTCTGCGCCCCTGCCCGCCGCCACCGCGCACCCGGCAGCAGCAGCGCACGCCGCACATCACCCCGCGGTGCACCACCCCATCctgccgcctgccgccgcagcggctgctgccgccgctgcagccg +i panTro2.chr21 C 0 C 0 +s mm8.chr16 91115780 184 + 98252459 GAGATCTACGGGGGTCACCACGCCGGCTTCCACCCATCGGCCTGTGGCGGGCTGGCACACTCGGCGCCTCTACCCACCGCCACGGCGCACCCCGCGGCCGCCGCGCACGCCGCGCACCACCCGGCCGTGCACCACCCCATCCTCCCTCccgcagccgccgccgccgccgcagccgccgccgccg +i mm8.chr16 C 0 C 0 + +a score=235994.0 +s hg18.chr21 33321746 103 + 46944323 cggctgTGTCCAGCGCCTCTCTGCCCGGATCCGGGCTGCCGTCGGTCGGCTCCATCCGTCCACCGCACGGCCTACTCAAGTCTCCGTCTGCTgccgcggccgc +s mm8.chr16 91115964 103 + 98252459 cAGCGGTGTCCAGCGCCTCTCTACCGGGCTCCGGGCTGTCCTCGGTCGGATCCATCCGGCCTCCGCACGGCCTGCTCAAGTCACCGTCGGCAGCCGCAGCCGC +i mm8.chr16 C 0 C 0 +s panTro2.chr21 32770787 103 + 46489110 cggctgTGTCCAGCGCCTCTCTGCCCGGATCCGGGCTGCCGTCGGTCGGCTCCATCCGTCCACCGCACGGCCTACTCAAGTCTCCGTCTGCTGCCGCAgccgc +i panTro2.chr21 C 0 C 0 + +a score=336560.0 +s hg18.chr21 33321849 74 + 46944323 cccgctggggggcgggggcggcggcAGTGGGGCGAGCGGGGGCTTCCAGCACTGGGGCGGCATGCCCTGCCCCT +s panTro2.chr21 32770890 74 + 46489110 cccgctggggggcgggggcggcggcAGTGGGGCGAGCGGGGGCTTCCAGCACTGGGGCGGCATGCCCTGCCCCT +i panTro2.chr21 C 0 C 0 +s mm8.chr16 91116067 74 + 98252459 CCCTCTCGGAGGCGGGGGTGGAGGCAGCGGTGGCAGCGGTGGCTTCCAGCACTGGGGCGGCATGCCGTGCCCCT +i mm8.chr16 C 0 C 0 + +a score=333126.0 +s hg18.chr21 33321923 30 + 46944323 GCAGCATGTGCCAGGTGCCGCCGCCGCACC +s panTro2.chr21 32770964 30 + 46489110 GCAGCATGTGCCAGGTGCCGCCGCCGCACC +i panTro2.chr21 C 0 C 0 +s mm8.chr16 91116141 30 + 98252459 GCAGCATGTGCCAGGTGCCGCCGCCGCACC +i mm8.chr16 C 0 C 0 + +a score=245579.0 +s hg18.chr21 33321953 40 + 46944323 ACCACGTGTCGGCTATGGGCGCCGGCAGCCTGCCGCGCCT +s panTro2.chr21 32770994 40 + 46489110 ACCACGTGTCGGCCATGGGCGCCGGCAGCCTGCCGCGCCT +i panTro2.chr21 C 0 C 0 +s mm8.chr16 91116171 40 + 98252459 ACCACGTGTCGGCTATGGGCGCCGGCACCTTGCCGCGCCT +i mm8.chr16 C 0 C 0 + +a score=-238175.0 +s hg18.chr21 33321993 19 + 46944323 CACCTCCGACGCCAAGTGA +s panTro2.chr21 32771034 19 + 46489110 CACCTCCGACGCCAAGTGA +i panTro2.chr21 C 0 C 0 +s mm8.chr16 91116211 19 + 98252459 CACCTCCGACGCCAAGTGA +i mm8.chr16 C 0 C 0 + +a score=157215.0 +s hg18.chr21 13199327 2 - 46944323 GA +s mm8.chr16 6787486 2 - 98252459 GA +s panTro2.chr21 13299591 2 - 46489110 GA + +a score=753161.0 +s hg18.chr21 13199283 44 - 46944323 CACTCTGATCTACAAATTTGGAAGAACCGAAGAGCTATGGACCT +s panTro2.chr21 13299547 44 - 46489110 CACTCTGATCTACAAATTTGGAAGAACCGAAGAGCTATGGACCT +s mm8.chr16 6787442 44 - 98252459 CACTCTGATCTACAAATTTGGAAGAACTGAAGAGCTCTGGGCCT + +a score=254771.0 +s hg18.chr22 30120223 42 + 49691432 ctcccatgctgtggaagctttgctattttggtcttcgcaatg +s panTro2.chr22 30280431 42 + 50165558 ctcccatgctgtggaagctttgttattttgctcttcgcaaag +i panTro2.chr22 C 0 C 0 + +a score=154402.0 +s hg18.chr22 19531009 4 - 49691432 CAAT +s panTro2.chr22 19843351 4 - 50165558 CAGT +s mm8.chr11 3149702 4 + 121798632 CAGT + +a score=61287.0 +s hg18.chr22 19530974 35 - 49691432 ATCTCCCAAAATAGGTTAGCCTTGCGGGGAGTGAT +s panTro2.chr22 19843316 35 - 50165558 ATCTCCCAAAATAGGTTAGCCTTGCGGGGAGTGAT + +a score=74044.0 +s hg18.chr22 19530840 134 - 49691432 ttactatccccatgttacatgaggaaactgaggctcataaaggttgggtaatttgttcagggctccacagctaactagaggtggacctgcaatttcaaaccctgatctgcctggtcggagtacttaa-ttacATG +s panTro2.chr22 19843181 135 - 50165558 ttactatccccatgttacatgaggaaactgaggctcataaaggttgggtaatttgttcagggctccacagctaactagaggtggacctgcaacttcaaaccctgatctgcctgGTCGGAGTACTTAAATTACATG + +a score=81981.0 +s hg18.chr22 19530787 53 - 49691432 aagtaccatctccctccattactaacaatcaccaccgcagaaagtaagtgcta +s panTro2.chr22 19843128 53 - 50165558 aagtaccatctccctccattactaacaatcaccaccgcagaaagtaagtgcta + +a score=-1554.0 +s hg18.chr22 19530771 16 - 49691432 acagtatttgacatat +s panTro2.chr22 19843112 16 - 50165558 acagtatttgacatgt + +a score=90207.0 +s hg18.chr22 30665273 17 + 49691432 GGCCTACAGTGGGAGAA +s panTro2.chr22 30838165 17 + 50165558 GGCCTACAGTGGGAGAA +i panTro2.chr22 I 13 C 0 + +a score=642220.0 +s hg18.chr22 30665290 70 + 49691432 AAAGTTAAAATCCTATCTGGGTGACATTATTAATAATTTGTGGACAGGCGGCTGCTCCAGCTCAAGATGG +s panTro2.chr22 30838182 70 + 50165558 AAAGTTAAAATCCTATCTGGGTGACATTATTAATAATTTGTGGACAGGCGGCTGCTCCAGCTCAAGATGG +i panTro2.chr22 C 0 C 0 + +a score=271624.0 +s hg18.chr22 18752166 212 - 49691432 ctgacaaaggagttgtatccggaataaaaagaccaacaggccaactttaaaactcaaaaaaaaaaatgacaCTTGGAGAAGAGCTTCAAGGTGACTGACtagaggtgcccaacattcgtctcctccacaaagaaggagcaaaacagataatcacatgtcaaatagagcatctaacagagaatgctggaattcagcggggaagtgacagaacc +s panTro2.chr22 19062041 173 - 50165558 ctgacaaaggagttgtatctggaataAAAAGACCAACAGGCCAActt---------------------------------------caaggtgactgactagaggtgcccaacattcgtctcctccacaaagaaggagcaaaacagataatcacatgtcaaatagagcatctaacagagaatgctggaattcagcggggaagtgacagaacc + +a score=489900.0 +s hg18.chr5 131424298 81 + 180857866 ATGAGCCGCCTGCCCGTCCTGCTCCTGCTCCAACTCCTGGTCCGCCCCGGACTCCAAGCTCCCA----TGACCCAGACAACGCCC +s panTro2.chr5 133682646 81 + 183994906 ATGAGCCGCCTGCCCGTCCTGCTCCTGCTCCAACTCCTGGTCCGCCCCGGACTCCAAGCTCCCA----TGACCCAGACAACGTCC +i panTro2.chr5 C 0 C 0 +s mm8.chr11 67687980 73 - 121798632 ACCAGCATCCACACCATGCTGCTCCTGCTCCTGATGCTCTTCCACCTGGGACTCCAAGCTTCAATCAGTGGCC------------ +i mm8.chr11 C 0 I 19 + +a score=-86483.0 +s hg18.chr5 131424379 81 + 180857866 TTGAAGACAAGCTGGGTTAACTGCTCTAACATGATCGATGAAATTATAACACACTTAAAGCAGCCACCTTTGCCTTTGCTG +s panTro2.chr5 133682727 81 + 183994906 TTGAAGACAAGCTGGGTTAACTGCTCTAACATGATCGATGAAATTATAACACACTTAAAGCAGCCACCTTTGCCTTTGCTG +i panTro2.chr5 C 0 C 0 +s mm8.chr11 67688072 52 - 121798632 ----CAGAACGTTGA----ATTGCAGCTCTATTGTCAAGGAGATTATAG------GGAAGCTCCCA--------------- +i mm8.chr11 I 19 C 0 + +a score=1522676.0 +s hg18.chr5 49301194 71 - 180857866 TCTCCAATAAGTGGTTCCATGAACGAGGACAGGAGTTCTTGAGACCTTGTGGATCAACAGAAGTTGACTGA +s panTro2.chr5 50180989 71 - 183994906 TCTCCAATAAGTGGTTCCATGAACGAGGACAGGAGTTCTTGAGACCTTGTGGATCAACAGAAGTTGACTGA +s mm8.chr11 53974612 71 + 121798632 TCTCCAACAAGTGGTTCCATGAGCGAGGACAGGAGTTCTTAAGACCTTGTGGAACAACGGAAGTTGATTGA + +a score=291108.0 +s hg18.chr5 131621326 30 + 180857866 ATGCCCCATTCCGTGACCCTGCGCGGGCCT +s panTro2.chr5 133877364 30 + 183994906 ATGCCCCATTCCGTGACCCTGCGCGGGCCT +i panTro2.chr5 C 0 C 0 +s mm8.chr11 67886277 30 - 121798632 ATGACCCACTCGGTGACCCTGCGCGGCCCT +i mm8.chr11 C 0 C 0 + +a score=990690.0 +s hg18.chr5 131621356 63 + 180857866 TCGCCCTGGGGCTTCCGCCTGGTGGGCGGCCGGGACTTCAGCGCGCCCCTCACCATCTCACGG +s panTro2.chr5 133877394 63 + 183994906 TCGCCCTGGGGCTTCCGCCTGGTGGGCGGCCGGGACTTCAGCGCGCCCCTCACCATCTCACGG +i panTro2.chr5 C 0 C 0 +s mm8.chr11 67886307 63 - 121798632 TCACCCTGGGGCTTCCGCCTGGTGGGCGGCCGGGACTTCAGTGCTCCCCTCACCATCTCGCGG +i mm8.chr11 C 0 C 0 + +a score=519601.0 +s hg18.chr5 49010271 54 - 180857866 CTGCTGACCCCA---GTCCGGT---TGCCCTCCATCCAGGCCATTCCCTGTGCACCGTAG +s panTro2.chr5 49887369 54 - 183994906 CTGCTGACCCCA---GTCCGGT---TGCCCTCCATCCAGGCCATTCCCTGTGCACCGTAG +s mm8.chr11 53619809 60 + 121798632 CTGCTGGGCAACTCTGTGAGGCTGCCGCCCTCTATTCAGGCCATTCCTTGTGCACCATAG + +a score=431236.0 +s hg18.chr5 49010219 52 - 180857866 ACAGCGTGTCTTCACAGATCTGAAGAACATGGATGCCACC---TGGCTGGACAGC +s panTro2.chr5 49887317 52 - 183994906 ACAGCGTGTCTTCACAGATCTGAAGAACATGGATGCCACC---TGGCTGGACAGC +s mm8.chr11 53619754 55 + 121798632 ACAACATGTCTTCACGGAGATGAAGAATATGGACTCCATCATGTGGATGGACAGC + +a score=274608.0 +s hg18.chr5 49010200 19 - 180857866 GGGATATTGGGCTGAGTCT +s panTro2.chr5 49887298 19 - 183994906 GGGATATTGGGCTGAGTCT +s mm8.chr11 53619735 19 + 121798632 GGGACATTGGGATAGGCAT + +a score=3488854.0 +s hg18.chr6 62600248 144 - 170899992 TTGGAAGTTCATGAGGCTAAGCCTGTGCCAGAAAATCACCCACAGTGGGATACAGCAATAGAGGGGGATGAAGACCAGGAGGACAGTGAGGGCTTTGAAGATAGCTTTGAGGAAGAAGAGGAGGAAGAAGAAGATGATGACTAA +s panTro2.chr6 64206236 144 - 173908612 TTGGAAGTTCATGAGGCTAAGCCTGTGCCAGAAAATCACCCACAGTGGGATACAGCAATAGAGGGGGATGAAGACCAGGAGGACAGTGAGGGCTTTGAAGATAGCTTTGAGGAAGAAGAGGAGGAAGAAGATGATGATGACTAA +s mm8.chr10 42517305 144 + 129959148 TTGGAAGTTCATGAGGCCAAGCCTGTGCCAGAAAACCACCCACAGTGGGACACAGCGATAGAAGGTGACGAAGACCAGGAAGACAGTGAAGGATTTGAAGACAGCTTTGAGGAAGAGGAGGAGGAAGAGGAAGGTGGAGACTAA + +a score=673541.0 +s hg18.chr6 108594662 25 + 170899992 ATGAGCAAGCCAGCCGGATCAACAA +s panTro2.chr6 109997450 25 + 173908612 ATGAGCAAGCCAGCCGGATCAACAA +i panTro2.chr6 C 0 C 0 +s mm8.chr10 87687827 25 - 129959148 ATGAGCAAGCCCGCCGGATCAACAA +i mm8.chr10 C 0 C 0 + +a score=2387325.0 +s hg18.chr6 62259841 106 - 170899992 GGTCGCTGGTCATCCTCTGGCACAGAACGAACGTTGTCTTCACATGTTTTTACAAGATGAAATAATAGATAAAAGCTATACTCCATCTAAAATAAGACATGCCTGA +s panTro2.chr6 63864488 106 - 173908612 GGTCGCTGGTCATCCTCTGGCACAGAACGAACGTTGTCTTCACATGTTTTTACAAGATGAAATAATAGATAAAAGCTATACTCCATCTAAAATAAGACATGCCTGA +s mm8.chr10 42223067 106 + 129959148 GGTCGCTGGTCATCCTCTGGCCCAGAATGAACGTTGTCTTCACATGTTTTTACAGGATGAAATTATAGATAAAAGCTATACTCCATCTAAAATAAGACATGCCTGA + +a score=684735.0 +s hg18.chr6 108722976 80 + 170899992 ATGGCGGCCTCCTGGTCGCTCTTGGTTACCCTGCGCCCCTTAGCACAGAGCCCGCTGAGAGGGAGATGTGTTGGGTGCGG +s panTro2.chr6 110129713 80 + 173908612 ATGGCGGCCTCCTGGTCGCTCTTGGTTACCCTGCGCCCCTTAGCACAGAGCCCGCTGAGAGGGAGATGTGTTGGGTGCGG +i panTro2.chr6 C 0 C 0 +s mm8.chr10 87792332 80 - 129959148 ATGGCGGCCTCCTGGTCGCCCTTGGTTACTCTGCGCTCCGCCGCGCGCAGCCGGCTGACTGGGAGAGGTGTTGGGTGCGG +i mm8.chr10 C 0 C 0 + +a score=301881.0 +s hg18.chr6 108723056 59 + 170899992 GGCCTGGGCCGCCGCTCTCGCTCCTCTGGCCACCGCCCCTGGGAAGCCCTTTTGGAAAG +s panTro2.chr6 110129793 59 + 173908612 GGCCTGGGCCGCCGCTCTCGCTCCTCTGGCCACCGCCCCTGGGAAGCCCTTTTGGAAAG +i panTro2.chr6 C 0 C 0 +s mm8.chr10 87792412 59 - 129959148 GGCGCGGGTCGTCGCAATCCCTCCTCCGGCCCCTGGCCCTGGGAAACCCCTGTGGAAAG +i mm8.chr10 C 0 C 0 + +a score=77769.0 +s hg18.chr7 113660517 150 + 158821424 acaatatttttacatgtacaaaaggagtgtttaggattcctatagtgaaattaaataa--aaatagtatttcatcatttcatctttatcctctgcatttttactcttgtgtatgtcttatacaaaacagagtatataaaatatttaagtata +s panTro2.chr7 114366363 150 + 160261443 acaatatttttacatgtacaaaaggagcatttaggattcctatagtgaaattaaataa--aaatagtatttcatcatttcatctttatcctctgcatttttactgttgtgtatgtcttatacaaaacagagtatataaaatatttaagtata +i panTro2.chr7 C 0 C 0 +s mm8.chr6 15003289 119 + 149525685 TCAATA-TTTTGCAAGTTCAAAGG---TATTTTGCATTTATATAGCAAAGTTAAACTATTAA-----------------CATATCTGTACT------------TTTTGTATATGTCTGATATAGGACAGATGATATAAAATATTTAGGTTTA +i mm8.chr6 I 216 C 0 + +a score=225170.0 +s hg18.chr7 113660667 18 + 158821424 gtagcacttgtatataaa +s panTro2.chr7 114366513 18 + 160261443 gtagcacttgtatataaa +i panTro2.chr7 C 0 C 0 +s mm8.chr6 15003408 18 + 149525685 GCAGTGCTTTTATATAAA +i mm8.chr6 C 0 C 0 + +a score=109967.0 +s hg18.chr7 42309182 83 - 158821424 AA---ACAGAAAAAATGACAACCTAAAACTGATTTGCTCCTACCGCTTTTGAGAAAAGTAAAAACATAAAATATAATTTTATTCTC +s panTro2.chr7 42970029 83 - 160261443 AA---ACAGAAAAAATGATAACCTAAAACTGATTTGCTCCTACCGCTTTTGAGAAAAGTAAAAACATAAAATATAATTTTATTCTC +s mm8.chr6 131770695 82 - 149525685 CACTGAGGGGGAGGAGGACAACCTGAAATCCATTTGCTCTGATCAGATTTCATGAA----CGGAGATGAAATGTGTTTCTCTCCCA + +a score=102283.0 +s hg18.chr7 42309126 56 - 158821424 CACAGATAGACATA-CCAAATTACAGAGAACAGGTATCTACTGTTCTAAAAACCTGG +s panTro2.chr7 42969973 56 - 160261443 CACAGATAGACATA-CCAAATTACAGAGAACAGGTATCTACTGTTCTAAAAACCTGG +s mm8.chr6 131770639 56 - 149525685 CATAGGTGGGCACAGCCAAATGACAGAAGCTAAGAACCTATTGTTCTAAAA-CCAGC + +a score=19014.0 +s hg18.chr7 42309086 40 - 158821424 CTTTTCTTAGGAACAAGCGCCAGGACTGACTTAAGCATTA +s panTro2.chr7 42969933 40 - 160261443 CTTTTCTTAGGAACAAGCGCCAGGACTGACTTAAGCATTA +s mm8.chr6 131770600 39 - 149525685 GGTTTCTTAGGATCCATTACTGTGAAAGCTGC-TGCATGA + +a score=57850.0 +s hg18.chr7 42309063 23 - 158821424 ATATGTATTTGCCTCTTATTTTC +s mm8.chr6 131770575 23 - 149525685 GTATGTACCTGTCGCCCACTTCC +s panTro2.chr7 42969910 23 - 160261443 ATATGTATTTGCCTCTTATTTTC + +a score=41852.0 +s hg18.chr7 42309040 23 - 158821424 ATTCTTTTTCTTGTACAGAATCA +s panTro2.chr7 42969887 23 - 160261443 ATTCTTTTTCTTGTACAGAATCA +s mm8.chr6 131770552 23 - 149525685 CTTCTCCTGCTTTTACAGTGCGG + +a score=45100.0 +s hg18.chr7 42309035 5 - 158821424 CCTTT +s panTro2.chr7 42969882 5 - 160261443 CCTTT +s mm8.chr6 131770535 5 - 149525685 TAATT + +a score=1784527.0 +s hg18.chr7 116714099 53 + 158821424 T-------GTTTTCGTAAGTTGGAAAAGTTTGACTGGCACAGGAAAG-CATGTCCCATTAA +s panTro2.chr7 117499706 53 + 160261443 T-------GTTTTCATAAGTTGGAAAAGTTTGACTGGCACAGGAAAG-CATGTCCCATTAA +i panTro2.chr7 C 0 C 0 +s mm8.chr6 17948973 59 + 149525685 TTTTATTCATTTTCCTAGCTCAG--AGGTTTGACTGGCACAGGACAGCCAGGTCCTGTTAA +i mm8.chr6 C 0 C 0 + +a score=193794.0 +s hg18.chr7 41875637 246 - 158821424 T-CTATATATTTAAGTCTATGAAAGACATATATATACACATATGTATATGTtaataatatataatatagcctatta-----tatattataatcatatatataaattattatattatttatagtattatatatttatttagaataaatattactatattattatataacatatgttatatacaattataattataatatatattgtattatatattataataATGGGTTAGAGACATATATGTGACATATATA +s panTro2.chr7 42526447 252 - 160261443 TGCTATATATTTAAGTCTATGAAAGacatatatatacacatatgcatatattaataatatataatatagcctattatatattatattataatcatatatataaattattatattatttatagtgttatatgtttatttagaataaatattactatattattatataacatatgttatatacaattataattataatatatgttatattatatattataataataggttaGAGACATATATGTGACATATATA + +a score=4204045.0 +s hg18.chr8 27393549 146 - 146274826 CCCAGCGACAGAGCTGCATGAATACGTTTGCCAGCTGGTTTGGCTACATGCCGCTGATCCACTCTCAGATGAGGCTCGACCCCGTCCTCTTTAAAGACCAGGTCTCTATTTTGAGGAAGAAATACCGAGACATTGAGCGACTTTGA +s panTro2.chr8 27880503 146 - 145085868 CCCAGCGACAGAGCTGCATGAATACGTTTGCCAGCTGGTTTGGCTACATGCCGCTGATCCACTCTCAGATGAGGCTCGACCCCGTCCTCTTTAAAGACCAGGTCTCTATTTTGAGGAAGAAATACCGAGACATTGAGCGACTTTGA +s mm8.chr15 50593685 146 - 103492577 CCCAGCGACAGAGCTGCATGAATACATTTGCCAGCTGGTTTGGCTACATGCCGCTGATCCATTCTCAGATGAGGCTGGACCCGGTCCTCTTTAAAGACCAAGTCTCAATTCTGAGGAAGAAATACAGAGACATTGAACGACTTTGA + +a score=1001054.0 +s hg18.chr8 27393509 40 - 146274826 ACTTCTCGGGCTTCCCGTTGGGCTGACCCTGACCACTTTG +s panTro2.chr8 27880463 40 - 145085868 ACTTCTCGGGCTTCCCGTTGGGCTGACCCTGACCACTTTG +s mm8.chr15 50593645 40 - 103492577 ACTTCCCGAGCATCCCGCTGGGCCGACCCTGACCACTTTG + +a score=57001.0 +s hg18.chr9 128764156 6 + 140273252 catcaa +s panTro2.chr9 126736437 6 + 138509991 catcaa +i panTro2.chr9 C 0 C 0 +s mm8.chr2 148813766 6 - 181976762 CAGTAA +i mm8.chr2 C 0 C 0 + +a score=16385.0 +s hg18.chr9 128764162 27 + 140273252 actgtatctgtgggccatagttagcct-------------- +s panTro2.chr9 126736443 27 + 138509991 actgtatctgtgggccatagttagcct-------------- +i panTro2.chr9 C 0 C 0 +s mm8.chr2 148813772 31 - 181976762 ----------TGGCACAGGTACACCATTTTCCATGGAGGGA +i mm8.chr2 C 0 C 0 + +a score=76022.0 +s hg18.chr9 11485716 17 - 140273252 TTTTAcaa---gataatgta +s panTro2.chr9 11748557 17 - 138509991 TTTTACAA---GATAATGTA +s mm8.chr2 33142635 20 + 181976762 CTCTAAGAAATGACAATGGC + +a score=169894.0 +s hg18.chr9 11485632 84 - 140273252 aaatatataaatatCAAGGGAATTAAGTAACAACTCTATAATGTTATATTTGAATTGGAAAGATCAGTATTATATTAGTCAAAT +s panTro2.chr9 11748473 84 - 138509991 aaatatataaatatCAAGGGAATTAAGTAACAACTCTATAATGTTATATTTGAATTGGAAAGATCAGTATTATATTAGTCAAAT +s mm8.chr2 33142562 73 + 181976762 AAATACAAGAAAATCAAGATCCTTAGGGAACATCAGGATAAGGACAGGTAAGAGCTGGGAAGAGTGACT-----------CACC + +a score=100082.0 +s hg18.chr9 11485610 22 - 140273252 CCAAAATTGTCACTGtaaaata +s panTro2.chr9 11748451 22 - 138509991 CCAAAATTGTCACTGtaaaata +s mm8.chr2 33142540 22 + 181976762 CTAAAACTGCCATTGTCAAATA + +a score=31644.0 +s hg18.chr9 11485572 38 - 140273252 atG-----------ACGGGATAATAT----AAAGTAAG----TAATGTTGCTAGGAA +s panTro2.chr9 11748413 38 - 138509991 atG-----------ACGGGATAATAT----AAAGTAAG----TAATGTTGCTAGGAA +s mm8.chr2 33142484 56 + 181976762 GAGTGCACAGGCACGAGTTAGAACAACGCAGGAA-AAGTAACCAGTATTGTTAGGAA + +a score=59361.0 +s hg18.chr9 11485526 46 - 140273252 TAGTAGTAATATTCGtattattat---------------------ttttaaattattttacata----tat +s panTro2.chr9 11748367 46 - 138509991 TAGTAGTAATATTCGtattattat---------------------ttttaaattattttacata----tat +s mm8.chr2 33142413 71 + 181976762 TGACAATAATGGCCTTGCTATTTTAAAGCACCCAGCCCACCTCCACCCAGTGTGCATGCACATACATATGT + +a score=132295.0 +s hg18.chr9 11485487 39 - 140273252 TGCAAG---------AAAATGTTAAAATTTGACCAGCAGTCTACTGCT +s panTro2.chr9 11748328 39 - 138509991 TGCAAG---------AAAATGTTAAAATTTGACCAGCAGTCTACTGCT +s mm8.chr2 33142362 48 + 181976762 TGCAAACAGAACCACAAAGTGGGAAACTTGAACCTGCAGTCGGCCAGG + +a score=57825.0 +s hg18.chr9 11485468 19 - 140273252 AAGAAGTAAAAGAACTAAC +s panTro2.chr9 11748309 19 - 138509991 AAGAAGTAAAAGAACTAAC +s mm8.chr2 33142345 17 + 181976762 CAGAAGAAAGGGAAC--AC + +a score=350567.0 +s hg18.chr9 11485308 160 - 140273252 caggtactgGGATTACAACAGGGTATCTCAGTATGCAGACCCTCTAGAACCAAATTAGCATAACCCTCCTTTTCTGTCCTGGTGCTTCCAAAGACCTTTAAGGGAAAAGTCCAGGGGAGAGGCCC---ACT--TGGGTATGTAAGTAGTAGGAAAGAGAGAAGAC +s mm8.chr2 33142195 150 + 181976762 CAGGTACTGAGATTACACCAGGGCCTCTTGGAGTACAGACCTCC--------------AAAAACCAGCTGCCTGTGACCACCTTCTTCTGAAAACCT-TAGAGGCAAAGAAAAGATGGAAGGCCCAACCCATCAAGAGGTGTGAGAGGAAGGAGGGAGAGACAAC +s panTro2.chr9 11748149 160 - 138509991 caggtactgGGATTACAACAGGGTATCTCAGTATGCAGACCCTCTAGAACCAAATTAGCATAACCCTCCTTTTCTGTCCTGGTGCTTCCAAAGACCTTTAAGGGAAAAGTCCAGGGGAGAGGCCT---ACT--TGGGTATATAAGTAGTAGGAAAGAGAGAAGAC + +a score=-38935.0 +s hg18.chr9 11485292 16 - 140273252 attatgta-ctg-tgttc +s panTro2.chr9 11748133 16 - 138509991 attatgta-ctg-tgttc +s mm8.chr2 33142179 16 + 181976762 --TGAGCAGCTGCTACTC + +a score=73778.0 +s hg18.chr9 11485257 35 - 140273252 CATCCATTCACACtccactcattcaacaaatattt +s mm8.chr2 33142146 33 + 181976762 GTATTGGCCCTTCTCCACTCAG--GACAGATCCCC +s panTro2.chr9 11748098 35 - 138509991 CATCCATTCACACtccactcattcaacaaatattt + +a score=368197.0 +s hg18.chr9 11485084 173 - 140273252 GAATCTTCAAAAGGCTGAGCTCACCAGGAAATACCC-------TTGCTTTGCGGGAAGTGGTTACACCACAAAACAAGACACCCTGGTAATATCGCTCCTTTGGTTGGCACACGCCCTCGCTTGGCAGTGTGCCTAAACACAGCCAGATAATGTTCTGCTATGGCGCTTCCCCTTTCAGG +s panTro2.chr9 11747926 172 - 138509991 GAATCTTCAAAAGGCTGAGCTCACCAGGAAATACCC-------TTGCTTTGCGGGAAGTGGTTACACCAC-AAACAAGACACCCTGGTAATATCGCTCCTTTGGTTGGCACACCCCCTCGCTTGGCAGTGTGCCTAAACACAGCCAGATAATGTTCTGCTATGGCGCTTCCCCTTTCAGG +s mm8.chr2 33141997 149 + 181976762 AAATCTCCAAAAGGCTGAGCCCACCAGGCAAAACCCCTCTTTTTTTCTTTGGGAAAAGTGACCAC----------TGCGCACCCAGTAGACACTGCTCCT-GAGCTGTCCTGTCCTG--------------------AGTCAGTCAGAAAACACTGTGCCAAGATGCTTGCCCTCACTGG + +a score=735006.0 +s hg18.chr9 11484882 202 - 140273252 AGAGTCACCAGGGGACAGGGCAGTTATGGTTCCATATTTGTAACTTCCATTTTCCTTACTCTCTGCCAATCCTTAACTCACCGTCTGCCTGGCTTCCTCTAAGCCCTGAAATGATGTTCTTTGTGGTCCCCCTTGCAGAAACCAGCAGAAGTCATGAAAAGCCACAGCTCCACCCTCAGTTATCAACTGCATTTGGAAATGT +s panTro2.chr9 11747724 202 - 138509991 AGAGTCACCAGGGGACAGGGCAGTTATGGTTCCATATTTGTAACTTCCATTTTCCTTACTCTCTGCCAATCCTTAACTCACCGTCTGCCTGGCTTCCTCTAAGCCCTGAAATGATGTTCTTTGTGGTCCCCCTTGCAGAAACCAGCAGAAGTCATGAAAAGCCACAGCTCCACCCTCAGTTATCAACTGCATTTGGAAATGT +s mm8.chr2 33141834 163 + 181976762 -----TAGCAGGGATCAGCACAATCGTG-TCCCATGCTTGTGACCTCCACATTCCTTATACTCTGCCAGTCC------------------------TCCTGAGTCCTGGGATGAGGCG--CTGTGGTTACCCCA-CAGAGAAGAGCACAAGTCCTAGT--GCTACA-TTCCAGCCCCAGCTGTGGGAGCCACT---GAATTC + +a score=440472.0 +s hg18.chr9 11484776 106 - 140273252 GGGGTTCTAGGCCACAACTTGTAAGTTCAACACAGCTGTGAGATATTATGCTACAAAGCTATATCTGCATTAATACACCAATTTTTGATAAACTTGGTCACTCGTT +s panTro2.chr9 11747618 106 - 138509991 GGGGTTCTAGGCCACAACTTGTAAGTTCAACACAGCTGTGAGATATTATGCTACAAAGCTATATCTGCATTAATACACCAATTTTTGATAAACTTGGTCACTCGTT +s mm8.chr2 33141754 80 + 181976762 AG-------------------------CAGCCTAGCTATAAGCAGA-ATGCCACAGAATTACATGTACGTTAAGTTGCCAGCTCTTTATAAAACTGGTCACTTATT + +a score=157210.0 +s hg18.chr9 11484715 61 - 140273252 CCTGGCAGCCAGGAATCCACCCAGGAATCTACCCTGCAACCCAATCCACCACAGTGGCAAT +s mm8.chr2 33141702 52 + 181976762 CCTGGCAGGCAGGAGTCTAACCAGA------G-CTGTCACCCAGTT-ATCCAGGTC-CAAC +s panTro2.chr9 11747557 61 - 138509991 CCTGGCAGCCAGGAATCCACCCAGGAATCTACCCTGCAACCCAATCCACCACAGTGGCAAT + +a score=-50628.0 +s hg18.chr9 11484601 114 - 140273252 GTAAGGAGCTCTGGTAGAGACAAAACACCACCTTGAAAACATACCCTTTTAGAAGGCTGCTACCACCAGGACCTTCAGACAGACCTCCTTTACAATGCAGCCCTTGCCCCAAGC +s panTro2.chr9 11747443 114 - 138509991 GTAAGGAGCTCTGGTAGAGACAAAACACCACCTTGAAAACATACCCTTTTAGAAGGCTGCTACCACCAGGACCTTCAGACAGACCTCCTTTACAATGCAGCCCTTGCCCCGAGC +s mm8.chr2 33141592 110 + 181976762 GTAGGGAATACTG-TGGACACAAAATGCTATGCCAAAACATGCCAGGTCAAGCAGGATGCAGCCACCAGGACCCTCAAACAAAG-CCCTTCATGAGGTAGCGTCA--CCCGAGC + +a score=125989.0 +s hg18.chr9 11484506 95 - 140273252 ACAAAAACAGTTCTGACATTTAGACCAGCCTCTGAGACACTGCTGCGCCTTCAACTCCATAGGCTGGGAACTGGACATACTGACAGACAGATGTG +s panTro2.chr9 11747348 95 - 138509991 ACAAAAACAGTTCTGACATTTAGACCAGCCTCTGAGACACTGCTGCGCCTTCAACTCCATAGGCTGGGAACTGGACATACTGACAGACAGATGTG +s mm8.chr2 33141545 47 + 181976762 -----------------------------CTCTGAGGAGCTGTAGGAGCCTCCGTTCTGTG------------AGTATGA-------CAGACTTG + +a score=128122.0 +s hg18.chr9 11484395 111 - 140273252 AGCTCAGCTCTGACAGAACCCTGGGCTGAATAAAGCACAGGCTGTGCCCATTTTCAGCACATTCTAAGAACAGCAGTTTCCCCTTGATGCTGCTCCATGCTAAAACTAATG +s panTro2.chr9 11747237 111 - 138509991 AGCTCAGCTCTGACAGAACCCTGGGCTGAATAAAGCACAGGCTGTGCCCATTTTCAGCACATTCTAAGAACAGCAGTTTCCCCTTGATGCTGCTCCATGCTAAAACTAATG +s mm8.chr2 33141446 99 + 181976762 AGCTCAACTCTGATAGGGTCATGGGCTAAGTACAGCCAAGGCCATGTCCATTTCCAGCTCAGTTTGAGAACAG-AGATCCACCATGCTGGGGTCTGGTGC----------- + +a score=88798.0 +s hg18.chr9 11484289 106 - 140273252 acttgtcctaagtctccaagctag-aggggtgaggctgtgactcaacctcagcttcatcagatcaaagttcatgctcttCAAGCTGTGTGGCTTTAACAGACCCAGC +s panTro2.chr9 11747131 106 - 138509991 acttgtcctaagtctccaagctag-aggggtgaggctgcgactcaacctcagcttcatcagatcaaagttcatcctcttCAAGCTGTGTGGCTTTAACAGACCCAGC +s mm8.chr2 33141368 78 + 181976762 GT----CCAGCATC--TTAGCTGGGATGAGAGCAGCCACA-CCCAT-CCCAGCTCTGACAGAT-------------------GTTATATATAGTTATTAAGC--AGT + +a score=128280.0 +s hg18.chr9 11484174 115 - 140273252 gctttgtacaggcaccgcgctaagttcttacatgcccactgtaaggtaaaagc---------tatgacttccaccccccgccaactttacacatgagaaaatcaaggcataaagaaaatacatg +s panTro2.chr9 11747016 115 - 138509991 gctttgtacaggcaccgtactaagttcttacatgcccactgtaaggtaaaagc---------tatgatttccaccccccgccaactttacacatgagaaaatcaaggcataaagaaaatacatg +s mm8.chr2 33141283 85 + 181976762 ---------------------------CTGGGTAGCTGCTGTGAGTTcaaaacaaaacaaaacaaaaTCACATCTC-------CCAT---GCACAAGGAAACTATAAGATAATGAGTAAGGA-- + +a score=175099.0 +s hg18.chr9 11484116 58 - 140273252 ACAGTGCCTATTCAAACTATACATTGGTGAaatgatagccacgcatgactaggagctt +s panTro2.chr9 11746958 58 - 138509991 ACAGTGCCTATTCAAACTATACACTGGTGAaatgatagccacgcatgactaggagctt +s mm8.chr2 33141234 49 + 181976762 ACAGAGCCAGCTCAGACTGAGCAGCAG-----CAATAACCACAAATGACTGACA---- + +a score=294709.0 +s hg18.chr9 128882427 96 + 140273252 aacacattgcttgttgtaaaaattattcacactgaaaagaagtttataaagtaaaaagtgaatgtgccattcttcttctcccactttccagaggca +s panTro2.chr9 126860344 91 + 138509991 AACACATTGCTTGTTGTAAAAATTATTCACACT-----GAAGTTTATAAAGTAAAAAGTGAATGTGCCATTATTCTTCTCCCACTTTCCAGAGGCA +i panTro2.chr9 C 0 C 0 +s mm8.chr2 148901693 74 - 181976762 -------------CTGTGGAGATCATCCACATTACAAAGAAGTCTATAAAGTAAAATGTGAAAGT--CGCTCTGCCCCTCC-------CTCCGGCG +i mm8.chr2 C 0 C 0 + +a score=-107864.0 +s hg18.chr9 11336020 3 - 140273252 ACT +s panTro2.chr9 11593518 3 - 138509991 ACT +s mm8.chr2 33023385 3 + 181976762 ACT + +a score=-82513.0 +s hg18.chr9 11335985 35 - 140273252 ACGTGTCAATCTCCCTCCCCAAAGAGGGAGAGAGG +s panTro2.chr9 11593483 35 - 138509991 GCGTGTCAATCTCCCTCCCCAGAGAGGGAGAGAGG +s mm8.chr2 33023361 24 + 181976762 ---------TCTTCCTTCCC--ACCAGGAGGGAGG + +a score=80475.0 +s hg18.chr9 11335945 40 - 140273252 ACCAGTTTCTATGTTCAATGTGACCCAAACTCCAGGGGCT +s panTro2.chr9 11593443 40 - 138509991 ACCAGTTTCTATGTTCAATGTGACCCAAACTCCAGGAGCT +s mm8.chr2 33023351 10 + 181976762 GCCTGCCTCT------------------------------ + +a score=-9994.0 +s hg18.chr9 11335933 12 - 140273252 CTAGAA---------------------------ACAGCC +s panTro2.chr9 11593431 12 - 138509991 CTAGAA---------------------------ACAGCC +s mm8.chr2 33023313 38 + 181976762 -CAGAACAGTTTACGCTCCGTGAGACCTGCGGGCCAGCT + +a score=-18269.0 +s hg18.chr9 11335906 27 - 140273252 GAGTTTCTGCTTTCAGACATCTCTATA +s panTro2.chr9 11593404 27 - 138509991 GGGTTTCTGCTTTCAGAAATCTCTATA +s mm8.chr2 33023295 18 + 181976762 AAGCCTCTGCAG-CAGAAA-------- + +a score=163495.0 +s hg18.chr9 11335807 99 - 140273252 ATGTGGGCCCATCTTGCAAGGGCCACAGAGACAGGAATGAGAGGGTGGAGCCCACTTCTTCCCAGATACTCAAGTCCTTCCAAGGCCTTGTGACCCCAT +s panTro2.chr9 11593305 99 - 138509991 ATGTGGGCCCATCTTGCAAGGGCCACAGAGACAGGAATGAGAGGGTGGAGCCCACTTCTTCCCAGATACTCAAGTCCTTCCAAGGCCTTGTGACCCCAT +s mm8.chr2 33023200 95 + 181976762 ATCTTGGTCT-CCTGGCAAGACCACAGAGAATTAGATAGTGAGAATGGACCCCACCTCTTCTCAGCGACCCAAGTCCACT---GTCCTACAGGCTTCCA + +a score=100797.0 +s hg18.chrX 122745047 18 + 154913754 accatcaagaaagtaaaa +s panTro2.chrX 123190863 18 + 155361357 actatcaagaaagtaaaa +i panTro2.chrX C 0 I 759 + +a score=0.0 +s hg18.chrX 122745065 483 + 154913754 agacaacctacagaatgggagaaaatatttgcaaaccatatatctgacaagggacttttatctagaatgtataaccttaacattcaataatctttaaaaaaaaaaaagcccaatttgtttttttgtttttttttttgtttgttttttgttttttgtttttttttgagacggaggctcactctgtcacccaggctggagtgcagtggtgcgatctcagctcactgcaagctccgcctcccaggttcacgccattctcctgcctcagcctcccgagtagctgggactacaggcgcctgccaccacgcccagctaattttttgtatttttagtagagatggggtttcaccgtgttagccaggatggtctcgatctcctgacctcttgatctgcccaccttggcctcccaaagtgctgggattacaggtgagagccaccacgcccagccaaaaaaaaaagcccaattttcaaaaaggggcaaagggg + +a score=17937.0 +s hg18.chrX 122745548 189 + 154913754 ccgggcacggtggctcacgcctgtaatctcagcactttgggaggccaaggcagggggatcaggaggtcaggagttcgagaccagcctggccaaagcgaccagcctggccaacatggtgaaaccctgtctctactaaaaatacaaaaattagccgggcatggtggcagtacctgtaatcccagctactcg +s panTro2.chrX 123191640 189 + 155361357 ccgggcacggtggctcacgcctgtaatctcagcactttgggaggccaaggcagggggatcaggaggtcaggagttcgagaccagcctggccaaagggaccagcctggccaacatggtgaaaccctgtctctactaaaaatacaaaaattagccgggcatggtggcagtacctgtaatcccagctactcg +i panTro2.chrX I 759 C 0 + +a score=88563.0 +s hg18.chrX 122745737 187 + 154913754 ggaggctgaggcaggagaattgcttgaacccaggaggcagaggttgcagtaagctgagattgccccattgcactccagcctgggcaacagagtgagactcctactcaaaaaaaaaaaaaaaaaaaa-gttggcggatgcggggacagcaaagggcttaagtagacatttcttcaaagaagatatacaa +s panTro2.chrX 123191829 188 + 155361357 ggaggctgaggcaggagaattgcttgaacccaggaggcagaggttgcagtaagctgagattgccccattgcactccagcctgggcaacagagtgagactcctactcaaaaaaaaaaaaaaaaaaaaaGTTGGCAGATGCGGGGACAgcaaagggcttaagtagacatttcttcaaagaagatatacaa +i panTro2.chrX C 0 C 0 + +a score=60355.0 +s hg18.chrX 2264558 232 - 154913754 ctatctgggctcactgccagctccgcctcccgggttcacgccattcttctgcctcagcgtcccgagtagctgggactataggcgcccgccaccgcgcccggctaaatttttgtatttttagtagagatggggtttcaccctgttagccaggatggtctcgacctcctgacctcgtgatctgcccgcctcaccctcccaaagtgctgggatgccaggcgggagcccccgcgcc +s panTro2.chrX 2180049 232 - 155361357 ctctctgggctcactgccagctctgcctcccgggttcatgccattcttctgcctcagcgtcccgagtagctgggactacaggcgcccgcccccgcgcccggctaaatttttgtatttttagtagagatggggtttcaccctgttagccaggatggtctcgacctcctgacctcgtgatctgcccgcctcaccctcccaaagtgctgggattacaggcgtgagccaccgtgcc + +a score=-54866.0 +s hg18.chrX 152691446 7 + 154913754 TCAGAAC +s panTro2.chrX 153225439 7 + 155361357 TCAGAAC +i panTro2.chrX C 0 C 0 +s mm8.chrX 70018668 2 + 165556469 -----GC +i mm8.chrX C 0 C 0 + +a score=-88144.0 +s hg18.chrX 152691453 18 + 154913754 CGGAGGGCCTTGGGCATG +s mm8.chrX 70018670 18 + 165556469 TGGAGGGTCTTGAGGATG +i mm8.chrX C 0 C 0 +s panTro2.chrX 153225446 18 + 155361357 CGGAGGGCCTTGGGCATG +i panTro2.chrX C 0 C 0 + +a score=2270241.0 +s hg18.chrX 2219694 31 - 154913754 AGGCCAACCTGCGTAGCATGAGCTTGGGGTT +s panTro2.chrX 2133314 5 - 155361357 --------------------------GGGTT +s mm8.chrX 95535223 31 - 165556469 AGGCCAACCTGCGTAACATGAGCTTGGGGTT + +a score=-439513.0 +s hg18.chrX 2219662 32 - 154913754 AAGCCCTCACCCCCGCCACCGGGTCCAGGTCA +s mm8.chrX 95535191 32 - 165556469 AAGCCCCTGCCCCTGCCCCCACATTCAGGTCA + +a score=-528572.0 +s hg18.chrX 2219603 59 - 154913754 TGGCCCCACCCGCCCCTGGACAGAGCCCGCCCAGGGTGCGATGGGGGCAGGTCTGTGGC +s mm8.chrX 95535133 58 - 165556469 TGGCTCCTGAC-CTCAGGGCCTGATCCCACACCACCTGTATTAGCAATGGGTCAGAGGT + +a score=-746000.0 +s hg18.chrX 2219540 63 - 154913754 CTTTGTGCCTGTGTCCCTGCTGAGGACATCTCACTTTCCTTCCC--CCCACCTGCTGGGGCTTCC +s mm8.chrX 95535080 53 - 165556469 ------------GGCCCTGGTGAGGATAGTCCTCAGATCTTCTCTGAGCCCACTCCTGGAGTTCC + +a score=-199075.0 +s hg18.chrX 2219515 25 - 154913754 CGGGGAGCCGGCCACAGGGTCAGGC +s mm8.chrX 95535063 17 - 165556469 TATGGAAGAAGCCCCAA-------- + +a score=1368003.0 +s hg18.chrX 2219491 24 - 154913754 TTCTCCACCATGGTCTCTGTCCTG +s mm8.chrX 95535039 24 - 165556469 TTCTCTACCATGGTCTCCGTCCTG + diff -r 62b897ca35ca -r 6a066b05c94f tools/maf/interval2maf.py --- a/tools/maf/interval2maf.py Tue Sep 29 21:50:44 2009 -0400 +++ b/tools/maf/interval2maf.py Tue Sep 29 21:51:51 2009 -0400 @@ -80,6 +80,8 @@ split_blocks_by_species = True if options.remove_all_gap_columns and options.remove_all_gap_columns == 'remove_all_gap_columns': remove_all_gap_columns = True + else: + remove_all_gap_columns = True #Finish parsing command line #Open indexed access to MAFs @@ -113,6 +115,8 @@ for block in blocks: block = maf_utilities.chop_block_by_region( block, src, region ) if block is not None: + if species is not None: + block = block.limit_to_species( species ) block = maf_utilities.orient_block_by_region( block, src, region ) if remove_all_gap_columns: block.remove_all_gap_columns() diff -r 62b897ca35ca -r 6a066b05c94f tools/maf/interval2maf.xml --- a/tools/maf/interval2maf.xml Tue Sep 29 21:50:44 2009 -0400 +++ b/tools/maf/interval2maf.xml Tue Sep 29 21:51:51 2009 -0400 @@ -88,6 +88,14 @@ <param name="split_blocks_by_species" value="dont_split_blocks_by_species"/> <output name="out_file1" file="fsa_interval2maf.dat" /> </test> + <test> + <param name="input1" value="1.bed" dbkey="hg18" ftype="bed"/> + <param name="maf_source" value="cached"/> + <param name="mafType" value="28_WAY_MULTIZ_hg18"/> + <param name="species" value="hg18,panTro2,mm8"/> + <param name="split_blocks_by_species" value="dont_split_blocks_by_species"/> + <output name="out_file1" file="interval2maf_3from28way.maf" /> + </test> </tests> <help> **What it does**

1 0

[hg] galaxy 2795: Allow XML includes. Fixes #131
by Nate Coraor 02 Oct '09

02 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/023ea1a1d38a changeset: 2795:023ea1a1d38a user: Kanwei Li <kanwei(a)gmail.com> date: Tue Sep 29 13:20:48 2009 -0400 description: Allow XML includes. Fixes #131 1 file(s) affected in this change: lib/galaxy/util/__init__.py diffs (42 lines): diff -r 30a175ace572 -r 023ea1a1d38a lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py Tue Sep 29 12:17:57 2009 -0400 +++ b/lib/galaxy/util/__init__.py Tue Sep 29 13:20:48 2009 -0400 @@ -23,7 +23,7 @@ from galaxy.util.docutils_ext.htmlfrag import Writer as HTMLFragWriter pkg_resources.require( 'elementtree' ) -from elementtree import ElementTree +from elementtree import ElementTree, ElementInclude pkg_resources.require( "wchartype" ) import wchartype @@ -87,7 +87,7 @@ def unique_id(KEY_SIZE=128): """ - Genenerates a unique ids + Generates an unique id >>> ids = [ unique_id() for i in range(1000) ] >>> len(set(ids)) @@ -97,8 +97,10 @@ return md5(id).hexdigest() def parse_xml(fname): - """Returns an parsed xml tree""" + """Returns a parsed xml tree""" tree = ElementTree.parse(fname) + root = tree.getroot() + ElementInclude.include(root) return tree def xml_to_string(elem): @@ -152,7 +154,7 @@ class Params: """ Stores and 'sanitizes' parameters. Alphanumeric characters and the - non-alpahnumeric ones that are deemed safe are let to pass through (see L{valid_chars}). + non-alphanumeric ones that are deemed safe are let to pass through (see L{valid_chars}). Some non-safe characters are escaped to safe forms for example C{>} becomes C{__lt__} (see L{mapped_chars}). All other characters are replaced with C{X}.

1 0

[hg] galaxy 2796: Reintroduce nginx upload module support.
by Nate Coraor 02 Oct '09

02 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/b819249af24d changeset: 2796:b819249af24d user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Sep 29 17:14:20 2009 -0400 description: Reintroduce nginx upload module support. http://www.grid.net.ru/nginx/upload.en.html The following config variables are added to universe_wsgi.ini: nginx_upload_store = Path to nginx upload store ex: = database/upload_store nginx_upload_path = URL (from root of the Galaxy server) to direct upload POSTs to ex: = /_upload The following nginx config supports such a configuration: location /_upload { upload_store /path/to/galaxy/database/upload_store; upload_pass_form_field "tool_id"; upload_pass_form_field "tool_state"; upload_pass_form_field "async_datasets"; upload_pass_form_field "^files_[0-9]+\|.*"; upload_pass_form_field "file_type"; upload_pass_form_field "dbkey"; upload_pass_form_field "runtool_btn"; upload_pass_form_field "ajax_upload"; upload_pass_form_field "upload_option"; upload_pass_form_field "library_id"; upload_pass_form_field "folder_id"; upload_pass_form_field "message"; upload_pass_form_field "roles"; upload_set_form_field "__${upload_field_name}__is_composite" "true"; upload_set_form_field "__${upload_field_name}__keys" "name path"; upload_set_form_field "${upload_field_name}_name" "$upload_file_name"; upload_set_form_field "${upload_field_name}_path" "$upload_tmp_path"; upload_pass_args on; upload_pass /_upload_done; } location /_upload_done { set $dst /tool_runner/index; if ($args ~ nginx_redir=([^&]+)) { set $dst $1; } rewrite "" $dst; } 10 file(s) affected in this change: lib/galaxy/config.py lib/galaxy/tools/__init__.py lib/galaxy/tools/actions/upload_common.py lib/galaxy/tools/parameters/basic.py lib/galaxy/web/controllers/library.py lib/galaxy/web/controllers/library_admin.py templates/admin/library/upload.mako templates/library/library_dataset_common.mako templates/library/upload.mako tools/data_source/upload.xml diffs (166 lines): diff -r 023ea1a1d38a -r b819249af24d lib/galaxy/config.py --- a/lib/galaxy/config.py Tue Sep 29 13:20:48 2009 -0400 +++ b/lib/galaxy/config.py Tue Sep 29 17:14:20 2009 -0400 @@ -89,9 +89,10 @@ raise ConfigurationError( "user_library_import_dir specified in config (%s) does not exist" % self.user_library_import_dir ) # Configuration options for taking advantage of nginx features self.nginx_x_accel_redirect_base = kwargs.get( 'nginx_x_accel_redirect_base', False ) - self.nginx_upload_location = kwargs.get( 'nginx_upload_store', False ) - if self.nginx_upload_location: - self.nginx_upload_location = os.path.abspath( self.nginx_upload_location ) + self.nginx_upload_store = kwargs.get( 'nginx_upload_store', False ) + self.nginx_upload_path = kwargs.get( 'nginx_upload_path', False ) + if self.nginx_upload_store: + self.nginx_upload_store = os.path.abspath( self.nginx_upload_store ) # Parse global_conf and save the parser global_conf = kwargs.get( 'global_conf', None ) global_conf_parser = ConfigParser.ConfigParser() diff -r 023ea1a1d38a -r b819249af24d lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Tue Sep 29 13:20:48 2009 -0400 +++ b/lib/galaxy/tools/__init__.py Tue Sep 29 17:14:20 2009 -0400 @@ -464,7 +464,11 @@ if input_elem: # Handle properties of the input form self.check_values = util.string_as_bool( input_elem.get("check_values", "true") ) - self.action = input_elem.get( "action", "/tool_runner/index") + self.nginx_upload = util.string_as_bool( input_elem.get( "nginx_upload", "false" ) ) + if self.nginx_upload and self.app.config.nginx_upload_path: + self.action = input_elem.get( "action", self.app.config.nginx_upload_path + "?nginx_redir=/tool_runner/index" ) + else: + self.action = input_elem.get( "action", "/tool_runner/index") self.target = input_elem.get( "target", "galaxy_main" ) self.method = input_elem.get( "method", "post" ) # Parse the actual parameters diff -r 023ea1a1d38a -r b819249af24d lib/galaxy/tools/actions/upload_common.py --- a/lib/galaxy/tools/actions/upload_common.py Tue Sep 29 13:20:48 2009 -0400 +++ b/lib/galaxy/tools/actions/upload_common.py Tue Sep 29 17:14:20 2009 -0400 @@ -23,6 +23,8 @@ f.file.close() upload_dataset['file_data'] = dict( filename = f.filename, local_filename = local_filename ) + elif type( f ) == dict and 'filename' and 'local_filename' not in f: + raise Exception( 'Uploaded file was encoded in a way not understood by Galaxy.' ) if upload_dataset['url_paste'].strip() != '': upload_dataset['url_paste'] = datatypes.sniff.stream_to_file( StringIO.StringIO( upload_dataset['url_paste'] ), prefix="strio_url_paste_" )[0] else: diff -r 023ea1a1d38a -r b819249af24d lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py Tue Sep 29 13:20:48 2009 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Tue Sep 29 17:14:20 2009 -0400 @@ -304,22 +304,21 @@ def get_html_field( self, trans=None, value=None, other_values={} ): return form_builder.FileField( self.name, ajax = self.ajax, value = value ) def from_html( self, value, trans=None, other_values={} ): - # TODO: Fix nginx upload module support # Middleware or proxies may encode files in special ways (TODO: this # should be pluggable) - #if type( value ) == dict: - # upload_location = self.tool.app.config.nginx_upload_location - # assert upload_location, \ - # "Request appears to have been processed by nginx_upload_module \ - # but Galaxy is not configured to recgonize it" - # # Check that the file is in the right location - # local_filename = os.path.abspath( value['path'] ) - # assert local_filename.startswith( upload_location ), \ - # "Filename provided by nginx is not in correct directory" - # value = Bunch( - # filename = value["name"], - # local_filename = local_filename - # ) + if type( value ) == dict: + upload_store = self.tool.app.config.nginx_upload_store + assert upload_store, \ + "Request appears to have been processed by nginx_upload_module \ + but Galaxy is not configured to recognize it" + # Check that the file is in the right location + local_filename = os.path.abspath( value['path'] ) + assert local_filename.startswith( upload_store ), \ + "Filename provided by nginx is not in correct directory" + value = dict( + filename = value["name"], + local_filename = local_filename + ) return value def get_required_enctype( self ): """ diff -r 023ea1a1d38a -r b819249af24d lib/galaxy/web/controllers/library.py --- a/lib/galaxy/web/controllers/library.py Tue Sep 29 13:20:48 2009 -0400 +++ b/lib/galaxy/web/controllers/library.py Tue Sep 29 17:14:20 2009 -0400 @@ -792,8 +792,13 @@ # Send the current history to the form to enable importing datasets from history to library history = trans.get_history() history.refresh() + # If we're using nginx upload, override the form action + action = web.url_for( controller='library', action='library_dataset_dataset_association' ) + if upload_option == 'upload_file' and trans.app.config.nginx_upload_path: + action = web.url_for( trans.app.config.nginx_upload_path ) + '?nginx_redir=' + action return trans.fill_template( '/library/upload.mako', upload_option=upload_option, + action=action, library_id=library_id, folder_id=folder_id, replace_dataset=replace_dataset, diff -r 023ea1a1d38a -r b819249af24d lib/galaxy/web/controllers/library_admin.py --- a/lib/galaxy/web/controllers/library_admin.py Tue Sep 29 13:20:48 2009 -0400 +++ b/lib/galaxy/web/controllers/library_admin.py Tue Sep 29 17:14:20 2009 -0400 @@ -487,8 +487,13 @@ # Send the current history to the form to enable importing datasets from history to library history = trans.get_history() history.refresh() + # If we're using nginx upload, override the form action + action = web.url_for( controller='library_admin', action='library_dataset_dataset_association' ) + if upload_option == 'upload_file' and trans.app.config.nginx_upload_path: + action = web.url_for( trans.app.config.nginx_upload_path ) + '?nginx_redir=' + action return trans.fill_template( '/admin/library/upload.mako', upload_option=upload_option, + action=action, library_id=library_id, folder_id=folder_id, replace_dataset=replace_dataset, diff -r 023ea1a1d38a -r b819249af24d templates/admin/library/upload.mako --- a/templates/admin/library/upload.mako Tue Sep 29 13:20:48 2009 -0400 +++ b/templates/admin/library/upload.mako Tue Sep 29 17:14:20 2009 -0400 @@ -32,4 +32,4 @@ ${render_msg( msg, messagetype )} %endif -${render_upload_form( 'library_admin', upload_option, library_id, folder_id, replace_dataset, file_formats, dbkeys, roles, history, )} +${render_upload_form( 'library_admin', upload_option, action, library_id, folder_id, replace_dataset, file_formats, dbkeys, roles, history, )} diff -r 023ea1a1d38a -r b819249af24d templates/library/library_dataset_common.mako --- a/templates/library/library_dataset_common.mako Tue Sep 29 13:20:48 2009 -0400 +++ b/templates/library/library_dataset_common.mako Tue Sep 29 17:14:20 2009 -0400 @@ -1,4 +1,4 @@ -<%def name="render_upload_form( controller, upload_option, library_id, folder_id, replace_dataset, file_formats, dbkeys, roles, history )"> +<%def name="render_upload_form( controller, upload_option, action, library_id, folder_id, replace_dataset, file_formats, dbkeys, roles, history )"> <% import os, os.path %> %if upload_option in [ 'upload_file', 'upload_directory' ]: <div class="toolForm" id="upload_library_dataset"> @@ -8,7 +8,7 @@ <div class="toolFormTitle">Upload a directory of files</div> %endif <div class="toolFormBody"> - <form name="upload_library_dataset" action="${h.url_for( controller=controller, action='library_dataset_dataset_association' )}" enctype="multipart/form-data" method="post"> + <form name="upload_library_dataset" action="${action}" enctype="multipart/form-data" method="post"> <input type="hidden" name="tool_id" value="upload1"/> <input type="hidden" name="tool_state" value="None"/> <input type="hidden" name="library_id" value="${library_id}"/> diff -r 023ea1a1d38a -r b819249af24d templates/library/upload.mako --- a/templates/library/upload.mako Tue Sep 29 13:20:48 2009 -0400 +++ b/templates/library/upload.mako Tue Sep 29 17:14:20 2009 -0400 @@ -32,4 +32,4 @@ ${render_msg( msg, messagetype )} %endif -${render_upload_form( 'library', upload_option, library_id, folder_id, replace_dataset, file_formats, dbkeys, roles, history, )} +${render_upload_form( 'library', upload_option, action, library_id, folder_id, replace_dataset, file_formats, dbkeys, roles, history, )} diff -r 023ea1a1d38a -r b819249af24d tools/data_source/upload.xml --- a/tools/data_source/upload.xml Tue Sep 29 13:20:48 2009 -0400 +++ b/tools/data_source/upload.xml Tue Sep 29 17:14:20 2009 -0400 @@ -14,7 +14,7 @@ ${output.dataset.dataset.id}:${output} #end while </command> - <inputs> + <inputs nginx_upload="true"> <param name="file_type" type="select" label="File Format" help="Which format? See help below"> <options from_parameter="tool.app.datatypes_registry.upload_file_formats" transform_lines="[ "%s%s%s" % ( line, self.separator, line ) for line in obj ]"> <column name="value" index="1"/>

1 0

[hg] galaxy 2792: Sample Form definitions:
by Nate Coraor 02 Oct '09

02 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/874817d9147a changeset: 2792:874817d9147a user: rc date: Mon Sep 28 13:37:14 2009 -0400 description: Sample Form definitions: - layout details added to csv file importer - form preview 3 file(s) affected in this change: lib/galaxy/web/controllers/forms.py lib/galaxy/web/controllers/requests_admin.py templates/admin/forms/show_form_read_only.mako diffs (236 lines): diff -r 40c3c7798b64 -r 874817d9147a lib/galaxy/web/controllers/forms.py --- a/lib/galaxy/web/controllers/forms.py Mon Sep 28 12:39:53 2009 -0400 +++ b/lib/galaxy/web/controllers/forms.py Mon Sep 28 13:37:14 2009 -0400 @@ -307,7 +307,7 @@ fields.append(self.__get_field(i, **kwd)) fields = fields else: - fields = self.__import_fields(trans, csv_file, form_type) + fields, layout = self.__import_fields(trans, csv_file, form_type) return name, desc, form_type, layout, fields def __update_current_form(self, trans, **kwd): name, desc, form_type, layout, fields = self.__get_form(trans, **kwd) @@ -325,6 +325,7 @@ ''' import csv fields = [] + layouts = set() try: reader = csv.reader(csv_file.file) if form_type == trans.app.model.FormDefinition.types.SAMPLE: @@ -337,6 +338,7 @@ 'type': row[4], 'selectlist': options, 'layout':row[6]}) + layouts.add(row[6]) else: for row in reader: options = row[5].split(',') @@ -353,7 +355,7 @@ message='Error in importing <b>%s</b> file' % csv_file, **kwd)) self.__imported_from_file = True - return fields + return fields, list(layouts) def __save_form(self, trans, fdc_id=None, **kwd): ''' diff -r 40c3c7798b64 -r 874817d9147a lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Mon Sep 28 12:39:53 2009 -0400 +++ b/lib/galaxy/web/controllers/requests_admin.py Mon Sep 28 13:37:14 2009 -0400 @@ -710,7 +710,11 @@ select_user.add_option('Select one', 'none', selected=True) else: select_user.add_option('Select one', 'none') - for user in trans.app.model.User.query().all(): + def __get_email(user): + return user.email + user_list = trans.app.model.User.query().all() + user_list.sort(key=__get_email) + for user in user_list: if not user.deleted: if userid == str(user.id): select_user.add_option(user.email, user.id, selected=True) diff -r 40c3c7798b64 -r 874817d9147a templates/admin/forms/show_form_read_only.mako --- a/templates/admin/forms/show_form_read_only.mako Mon Sep 28 12:39:53 2009 -0400 +++ b/templates/admin/forms/show_form_read_only.mako Mon Sep 28 13:37:14 2009 -0400 @@ -6,62 +6,126 @@ ${render_msg( msg, messagetype )} %endif +<%def name="render_grid( grid_index, grid_name, fields_dict )"> + %if grid_name: + <div class="toolFormTitle">${grid_name}</div> + %endif + <div style="clear: both"></div> + <table class="grid"> + <thead> + <tr> + %for index, field in fields_dict.items(): + <th> + ${field['label']} + <div class="toolParamHelp" style="clear: both;"> + <i>${field['helptext']}</i> + </div> + </th> + %endfor + <th></th> + </tr> + <thead> + <tbody> + <tr> + %for index, field in fields_dict.items(): + <td> + <div>${field['required']}</div> +## <div>${field['type']}</div> + </td> + %endfor + <th></th> + </tr> + %for index, field in fields_dict.items(): + <td> +## <div>${field['required']}</div> + <div><i>Type:</i></div> + <div>${field['type']}</div> + </td> + %endfor + <th></th> + </tr> + <tr> + %for index, field in fields_dict.items(): + <td> + %if field['type'] == 'SelectField': + <div><i>Options:</i></div> + %for option in field['selectlist']: + <div>${option}</div> + %endfor + %endif + </td> + %endfor + <th></th> + </tr> + <tbody> + </table> +</%def> + <div class="toolForm"> <div class="toolFormTitle">${form.name} - <i>${form.desc}</i></div> <form name="library" action="${h.url_for( controller='forms', action='manage' )}" method="post" > - <table class = "grid"> - <tbody> - %for index, field in enumerate(form.fields): - <tr> - <td> - <div class="form-row"> - <label>${1+index}. Label</label> - <a>${field['label']}</a> - %if field['type'] == 'SelectField': - <a id="${field['label']}-popup" class="popup-arrow" style="display: none;">▼</a> - %for option in field['selectlist']: - <div popupmenu="${field['label']}-type-popup"> - <a class="action-button" href="" >${option}</a> - </div> - %endfor - %endif - </div> - </td> - <td> - <div class="form-row"> - <label>Help text </label> - %if not field['helptext']: - <a><i>No helptext</i></a> - %else: - <a>${field['helptext']}</a> - %endif - </div> - </td> - <td> - <div class="form-row"> - <label>Type:</label> - <a>${field['type']}</a> - %if field['type'] == 'SelectField': - <a id="fieldtype-popup" class="popup-arrow" style="display: none;">▼</a> - %for option in field['selectlist']: - <div popupmenu="type-popup"> - <a class="action-button" href="" >${option}</a> - </div> - %endfor - %endif - </div> - </td> - <td> - <div class="form-row"> - <label>Required?</label> - <a>${field['required']}</a> - </div> - </td> - </tr> + %if form.type == trans.app.model.FormDefinition.types.SAMPLE: + %if not len(form.layout): + ${render_grid( 0, '', form.fields_of_grid( None ) )} + %else: + %for grid_index, grid_name in enumerate(form.layout): + ${render_grid( grid_index, grid_name, form.fields_of_grid( grid_name ) )} %endfor - </tbody> - </table> - ##<input type="submit" name="save_changes_button" value="Back"/> + %endif + %else: + <table class = "grid"> + <tbody> + %for index, field in enumerate(form.fields): + <tr> + <td> + <div class="form-row"> + <label>${1+index}. Label</label> + <a>${field['label']}</a> + %if field['type'] == 'SelectField': + <a id="${field['label']}-popup" class="popup-arrow" style="display: none;">▼</a> + %for option in field['selectlist']: + <div popupmenu="${field['label']}-type-popup"> + <a class="action-button" href="" >${option}</a> + </div> + %endfor + %endif + </div> + </td> + <td> + <div class="form-row"> + <label>Help text </label> + %if not field['helptext']: + <a><i>No helptext</i></a> + %else: + <a>${field['helptext']}</a> + %endif + </div> + </td> + <td> + <div class="form-row"> + <label>Type:</label> + <a>${field['type']}</a> + %if field['type'] == 'SelectField': + <a id="fieldtype-popup" class="popup-arrow" style="display: none;">▼</a> + %for option in field['selectlist']: + <div popupmenu="type-popup"> + <a class="action-button" href="" >${option}</a> + </div> + %endfor + %endif + </div> + </td> + <td> + <div class="form-row"> + <label>Required?</label> + <a>${field['required']}</a> + </div> + </td> + </tr> + %endfor + </tbody> + </table> + %endif </form> </div> </div> \ No newline at end of file

1 0

[hg] galaxy 2793: Association proxy for user preferences.
by Nate Coraor 02 Oct '09

02 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/389226e41780 changeset: 2793:389226e41780 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon Sep 28 18:57:25 2009 -0400 description: Association proxy for user preferences. 4 file(s) affected in this change: lib/galaxy/model/__init__.py lib/galaxy/model/mapping.py lib/galaxy/web/controllers/history.py lib/galaxy/web/framework/helpers/grids.py diffs (148 lines): diff -r 874817d9147a -r 389226e41780 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Mon Sep 28 13:37:14 2009 -0400 +++ b/lib/galaxy/model/__init__.py Mon Sep 28 18:57:25 2009 -0400 @@ -1316,11 +1316,9 @@ pass class UserPreference ( object ): - def __init( self, user_id=None, name=None, value=None ): - self.user_id = user_id + def __init__( self, name=None, value=None ): self.name = name self.value = value - ## ---- Utility methods ------------------------------------------------------- diff -r 874817d9147a -r 389226e41780 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Mon Sep 28 13:37:14 2009 -0400 +++ b/lib/galaxy/model/mapping.py Mon Sep 28 18:57:25 2009 -0400 @@ -14,6 +14,8 @@ from galaxy.model.custom_types import * from galaxy.util.bunch import Bunch from galaxy.security import GalaxyRBACAgent +from sqlalchemy.orm.collections import attribute_mapped_collection +from sqlalchemy.ext.associationproxy import association_proxy metadata = MetaData() context = Session = scoped_session( sessionmaker( autoflush=False, transactional=False ) ) @@ -754,10 +756,14 @@ stored_workflow_menu_entries=relation( StoredWorkflowMenuEntry, backref="user", cascade="all, delete-orphan", collection_class=ordering_list( 'order_index' ) ), - preferences=relation( UserPreference, backref="user", order_by=UserPreference.table.c.id), + _preferences=relation( UserPreference, backref="user", collection_class=attribute_mapped_collection('name')), # addresses=relation( UserAddress, # primaryjoin=( User.table.c.id == UserAddress.table.c.user_id ) ) ) ) + +# Set up proxy so that this syntax is possible: +# <user_obj>.preferences[pref_name] = pref_value +User.preferences = association_proxy('_preferences', 'value', creator=UserPreference) assign_mapper( context, Group, Group.table, properties=dict( users=relation( UserGroupAssociation ) ) ) diff -r 874817d9147a -r 389226e41780 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Mon Sep 28 13:37:14 2009 -0400 +++ b/lib/galaxy/web/controllers/history.py Mon Sep 28 18:57:25 2009 -0400 @@ -125,6 +125,8 @@ grids.GridColumnFilter( "All", args=dict( deleted='All' ) ), ] default_filter = dict( deleted="False", tags="All" ) + preserve_state = False + use_paging = True def get_current_item( self, trans ): return trans.get_history() def apply_default_filter( self, trans, query, **kwargs ): diff -r 874817d9147a -r 389226e41780 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Mon Sep 28 13:37:14 2009 -0400 +++ b/lib/galaxy/web/framework/helpers/grids.py Mon Sep 28 18:57:25 2009 -0400 @@ -25,7 +25,7 @@ preserve_state = False use_paging = False - num_rows_per_page = 5 + num_rows_per_page = 10 # Set preference names. cur_filter_pref_name = ".filter" @@ -51,18 +51,14 @@ base_sort_key = self.default_sort_key if self.preserve_state: pref_name = unicode( self.__class__.__name__ + self.cur_filter_pref_name ) - saved_filter_pref = trans.sa_session.query( UserPreference ).\ - filter_by( name=pref_name, user_id=trans.get_user().id ).first() - if saved_filter_pref: - saved_filter = from_json_string( saved_filter_pref.value ) + if pref_name in trans.get_user().preferences: + saved_filter = from_json_string( trans.get_user().preferences[pref_name] ) base_filter.update( saved_filter ) pref_name = unicode( self.__class__.__name__ + self.cur_sort_key_pref_name ) - saved_sort_key_pref = trans.sa_session.query( UserPreference ).\ - filter_by( name=pref_name, user_id=trans.get_user().id ).first() - if saved_sort_key_pref: - base_sort_key = from_json_string( saved_sort_key_pref.value ) - + if pref_name in trans.get_user().preferences: + base_sort_key = from_json_string( trans.get_user().preferences[pref_name] ) + # Build initial query query = self.build_initial_query( session ) query = self.apply_default_filter( trans, query, **kwargs ) @@ -70,14 +66,23 @@ # Maintain sort state in generated urls extra_url_args = {} + # Determine whether use_default_filter flag is set. + use_default_filter_str = kwargs.get( 'use_default_filter' ) + use_default_filter = False + if use_default_filter_str: + use_default_filter = use_default_filter_str.lower() == 'true' + # Process filtering arguments to (a) build a query that represents the filter and (b) builds a - # dictionary that denotes the current filter. + # dictionary that denotes the current filter. cur_filter_dict = {} for column in self.columns: if column.key: - # Look for filter criterion in kwargs; if not found, look in base filter. + # Get the filter criterion for the column. Precedence is (a) if using default filter, look there; (b) look in kwargs; and (c) look in + # base filter. column_filter = None - if "f-" + column.key in kwargs: + if use_default_filter and self.default_filter: + column_filter = self.default_filter.get( column.key ) + elif "f-" + column.key in kwargs: column_filter = kwargs.get( "f-" + column.key ) elif column.key in base_filter: column_filter = base_filter.get( column.key ) @@ -136,17 +141,11 @@ # Preserve grid state: save current filter and sort key. if self.preserve_state: pref_name = unicode( self.__class__.__name__ + self.cur_filter_pref_name ) - if not saved_filter_pref: - saved_filter_pref = UserPreference( name=pref_name ) - trans.get_user().preferences.append( saved_filter_pref ) - saved_filter_pref.value = unicode( to_json_string( cur_filter_dict ) ) + trans.get_user().preferences[pref_name] = unicode( to_json_string( cur_filter_dict ) ) + if sort_key: - if not saved_sort_key_pref: - pref_name = unicode( self.__class__.__name__ + self.cur_sort_key_pref_name ) - if not saved_sort_key_pref: - saved_sort_key_pref = UserPreference( name=pref_name ) - trans.get_user().preferences.append( saved_sort_key_pref ) - saved_sort_key_pref.value = unicode( to_json_string( sort_key ) ) + pref_name = unicode( self.__class__.__name__ + self.cur_sort_key_pref_name ) + trans.get_user().preferences[pref_name] = unicode( to_json_string( sort_key ) ) trans.sa_session.flush() # Render grid. @@ -294,4 +293,4 @@ for k, v in self.args.items(): rval[ "f-" + k ] = v return rval - \ No newline at end of file +

1 0

[hg] galaxy 2794: Asynchronous library upload.
by Nate Coraor 02 Oct '09

02 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/30a175ace572 changeset: 2794:30a175ace572 user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Sep 29 12:17:57 2009 -0400 description: Asynchronous library upload. 11 file(s) affected in this change: lib/galaxy/tools/actions/upload.py lib/galaxy/tools/actions/upload_common.py lib/galaxy/web/controllers/library.py lib/galaxy/web/controllers/library_admin.py lib/galaxy/web/controllers/library_dataset.py lib/galaxy/web/controllers/tool_runner.py static/june_2007_style/blue/library.css static/june_2007_style/library.css.tmpl templates/base_panels.mako templates/library/library_dataset_common.mako templates/library/library_item_info.mako diffs (678 lines): diff -r 389226e41780 -r 30a175ace572 lib/galaxy/tools/actions/upload.py --- a/lib/galaxy/tools/actions/upload.py Mon Sep 28 18:57:25 2009 -0400 +++ b/lib/galaxy/tools/actions/upload.py Tue Sep 29 12:17:57 2009 -0400 @@ -15,14 +15,12 @@ precreated_datasets = upload_common.get_precreated_datasets( trans, incoming, trans.app.model.HistoryDatasetAssociation ) incoming = upload_common.persist_uploads( incoming ) - json_file_path, data_list = upload_common.create_paramfile( trans, incoming, precreated_datasets, dataset_upload_inputs ) + uploaded_datasets = upload_common.get_uploaded_datasets( trans, incoming, precreated_datasets, dataset_upload_inputs ) upload_common.cleanup_unused_precreated_datasets( precreated_datasets ) - if not data_list: - try: - os.remove( json_file_path ) - except: - pass + if not uploaded_datasets: return 'No data was entered in the upload form, please go back and choose data to upload.' + json_file_path = upload_common.create_paramfile( uploaded_datasets ) + data_list = [ ud.data for ud in uploaded_datasets ] return upload_common.create_job( trans, incoming, tool, json_file_path, data_list ) diff -r 389226e41780 -r 30a175ace572 lib/galaxy/tools/actions/upload_common.py --- a/lib/galaxy/tools/actions/upload_common.py Mon Sep 28 18:57:25 2009 -0400 +++ b/lib/galaxy/tools/actions/upload_common.py Tue Sep 29 12:17:57 2009 -0400 @@ -31,7 +31,32 @@ params['files'] = new_files return params -def get_precreated_datasets( trans, params, data_obj ): +def handle_library_params( trans, params, folder_id, replace_dataset=None ): + library_bunch = util.bunch.Bunch() + library_bunch.replace_dataset = replace_dataset + library_bunch.message = params.get( 'message', '' ) + # See if we have any template field contents + library_bunch.template_field_contents = [] + template_id = params.get( 'template_id', None ) + library_bunch.folder = trans.app.model.LibraryFolder.get( folder_id ) + # We are inheriting the folder's info_association, so we did not + # receive any inherited contents, but we may have redirected here + # after the user entered template contents ( due to errors ). + if template_id not in [ None, 'None' ]: + library_bunch.template = trans.app.model.FormDefinition.get( template_id ) + for field_index in range( len( library_bunch.template.fields ) ): + field_name = 'field_%i' % field_index + if params.get( field_name, False ): + field_value = util.restore_text( params.get( field_name, '' ) ) + library_bunch.template_field_contents.append( field_value ) + else: + library_bunch.template = None + library_bunch.roles = [] + for role_id in util.listify( params.get( 'roles', [] ) ): + library_bunch.roles.append( trans.app.model.Role.get( role_id ) ) + return library_bunch + +def get_precreated_datasets( trans, params, data_obj, controller='root' ): """ Get any precreated datasets (when using asynchronous uploads). """ @@ -54,7 +79,7 @@ else: rval.append( data ) elif data_obj is trans.app.model.LibraryDatasetDatasetAssociation: - if not trans.app.security_agent.can_add_library_item( user, roles, data.library_dataset.folder ): + if controller == 'library' and not trans.app.security_agent.can_add_library_item( user, roles, data.library_dataset.folder ): log.error( 'Got a precreated dataset (%s) but this user (%s) is not allowed to write to it' % ( data.id, user.id ) ) else: rval.append( data ) @@ -78,127 +103,143 @@ data.state = data.states.ERROR data.info = 'No file contents were available.' -def new_history_upload( trans, uploaded_dataset ): +def new_history_upload( trans, uploaded_dataset, state=None ): hda = trans.app.model.HistoryDatasetAssociation( name = uploaded_dataset.name, extension = uploaded_dataset.file_type, dbkey = uploaded_dataset.dbkey, history = trans.history, create_dataset = True ) - hda.state = hda.states.QUEUED + if state: + hda.state = state + else: + hda.state = hda.states.QUEUED hda.flush() trans.history.add_dataset( hda, genome_build = uploaded_dataset.dbkey ) permissions = trans.app.security_agent.history_get_default_permissions( trans.history ) trans.app.security_agent.set_all_dataset_permissions( hda.dataset, permissions ) return hda -def new_library_upload( trans, uploaded_dataset, replace_dataset, folder, - template, template_field_contents, roles, message ): - if replace_dataset: - ld = replace_dataset +def new_library_upload( trans, uploaded_dataset, library_bunch, state=None ): + user, roles = trans.get_user_and_roles() + if not ( trans.app.security_agent.can_add_library_item( user, roles, library_bunch.folder ) \ + or trans.user.email in trans.app.config.get( "admin_users", "" ).split( "," ) ): + # This doesn't have to be pretty - the only time this should happen is if someone's being malicious. + raise Exception( "User is not authorized to add datasets to this library." ) + if library_bunch.replace_dataset: + ld = library_bunch.replace_dataset else: - ld = trans.app.model.LibraryDataset( folder=folder, name=uploaded_dataset.name ) + ld = trans.app.model.LibraryDataset( folder=library_bunch.folder, name=uploaded_dataset.name ) ld.flush() - trans.app.security_agent.copy_library_permissions( folder, ld ) + trans.app.security_agent.copy_library_permissions( library_bunch.folder, ld ) ldda = trans.app.model.LibraryDatasetDatasetAssociation( name = uploaded_dataset.name, extension = uploaded_dataset.file_type, dbkey = uploaded_dataset.dbkey, library_dataset = ld, user = trans.user, create_dataset = True ) - ldda.state = ldda.states.QUEUED - ldda.message = message + if state: + ldda.state = state + else: + ldda.state = ldda.states.QUEUED + ldda.message = library_bunch.message ldda.flush() # Permissions must be the same on the LibraryDatasetDatasetAssociation and the associated LibraryDataset trans.app.security_agent.copy_library_permissions( ld, ldda ) - if replace_dataset: + if library_bunch.replace_dataset: # Copy the Dataset level permissions from replace_dataset to the new LibraryDatasetDatasetAssociation.dataset - trans.app.security_agent.copy_dataset_permissions( replace_dataset.library_dataset_dataset_association.dataset, ldda.dataset ) + trans.app.security_agent.copy_dataset_permissions( library_bunch.replace_dataset.library_dataset_dataset_association.dataset, ldda.dataset ) else: # Copy the current user's DefaultUserPermissions to the new LibraryDatasetDatasetAssociation.dataset trans.app.security_agent.set_all_dataset_permissions( ldda.dataset, trans.app.security_agent.user_get_default_permissions( trans.user ) ) - folder.add_library_dataset( ld, genome_build=uploaded_dataset.dbkey ) - folder.flush() + library_bunch.folder.add_library_dataset( ld, genome_build=uploaded_dataset.dbkey ) + library_bunch.folder.flush() ld.library_dataset_dataset_association_id = ldda.id ld.flush() # Handle template included in the upload form, if any - if template and template_field_contents: + if library_bunch.template and library_bunch.template_field_contents: # Since information templates are inherited, the template fields can be displayed on the upload form. # If the user has added field contents, we'll need to create a new form_values and info_association # for the new library_dataset_dataset_association object. # Create a new FormValues object, using the template we previously retrieved - form_values = trans.app.model.FormValues( template, template_field_contents ) + form_values = trans.app.model.FormValues( library_bunch.template, library_bunch.template_field_contents ) form_values.flush() # Create a new info_association between the current ldda and form_values - info_association = trans.app.model.LibraryDatasetDatasetInfoAssociation( ldda, template, form_values ) + info_association = trans.app.model.LibraryDatasetDatasetInfoAssociation( ldda, library_bunch.template, form_values ) info_association.flush() # If roles were selected upon upload, restrict access to the Dataset to those roles - if roles: - for role in roles: + if library_bunch.roles: + for role in library_bunch.roles: dp = trans.app.model.DatasetPermissions( trans.app.security_agent.permitted_actions.DATASET_ACCESS.action, ldda.dataset, role ) dp.flush() return ldda -def create_paramfile( trans, params, precreated_datasets, dataset_upload_inputs, - replace_dataset=None, folder=None, template=None, - template_field_contents=None, roles=None, message=None ): +def new_upload( trans, uploaded_dataset, library_bunch=None, state=None ): + if library_bunch: + return new_library_upload( trans, uploaded_dataset, library_bunch, state ) + else: + return new_history_upload( trans, uploaded_dataset, state ) + +def get_uploaded_datasets( trans, params, precreated_datasets, dataset_upload_inputs, library_bunch=None ): + uploaded_datasets = [] + for dataset_upload_input in dataset_upload_inputs: + uploaded_datasets.extend( dataset_upload_input.get_uploaded_datasets( trans, params ) ) + for uploaded_dataset in uploaded_datasets: + data = get_precreated_dataset( precreated_datasets, uploaded_dataset.name ) + if not data: + data = new_upload( trans, uploaded_dataset, library_bunch ) + else: + data.extension = uploaded_dataset.file_type + data.dbkey = uploaded_dataset.dbkey + data.flush() + if library_bunch: + library_bunch.folder.genome_build = uploaded_dataset.dbkey + library_bunch.folder.flush() + else: + trans.history.genome_build = uploaded_dataset.dbkey + uploaded_dataset.data = data + return uploaded_datasets + +def create_paramfile( uploaded_datasets ): """ Create the upload tool's JSON "param" file. """ - data_list = [] json_file = tempfile.mkstemp() json_file_path = json_file[1] json_file = os.fdopen( json_file[0], 'w' ) - for dataset_upload_input in dataset_upload_inputs: - uploaded_datasets = dataset_upload_input.get_uploaded_datasets( trans, params ) - for uploaded_dataset in uploaded_datasets: - data = get_precreated_dataset( precreated_datasets, uploaded_dataset.name ) - if not data: - if folder: - data = new_library_upload( trans, uploaded_dataset, replace_dataset, folder, template, template_field_contents, roles, message ) - else: - data = new_history_upload( trans, uploaded_dataset ) - else: - data.extension = uploaded_dataset.file_type - data.dbkey = uploaded_dataset.dbkey - data.flush() - if folder: - folder.genome_build = uploaded_dataset.dbkey - folder.flush() - else: - trans.history.genome_build = uploaded_dataset.dbkey - if uploaded_dataset.type == 'composite': - # we need to init metadata before the job is dispatched - data.init_meta() - for meta_name, meta_value in uploaded_dataset.metadata.iteritems(): - setattr( data.metadata, meta_name, meta_value ) - data.flush() - json = dict( file_type = uploaded_dataset.file_type, - dataset_id = data.dataset.id, - dbkey = uploaded_dataset.dbkey, - type = uploaded_dataset.type, - metadata = uploaded_dataset.metadata, - primary_file = uploaded_dataset.primary_file, - extra_files_path = data.extra_files_path, - composite_file_paths = uploaded_dataset.composite_files, - composite_files = dict( [ ( k, v.__dict__ ) for k, v in data.datatype.get_composite_files( data ).items() ] ) ) - else: - try: - is_binary = uploaded_dataset.datatype.is_binary - except: - is_binary = None - json = dict( file_type = uploaded_dataset.file_type, - ext = uploaded_dataset.ext, - name = uploaded_dataset.name, - dataset_id = data.dataset.id, - dbkey = uploaded_dataset.dbkey, - type = uploaded_dataset.type, - is_binary = is_binary, - space_to_tab = uploaded_dataset.space_to_tab, - path = uploaded_dataset.path ) - json_file.write( to_json_string( json ) + '\n' ) - data_list.append( data ) + for uploaded_dataset in uploaded_datasets: + data = uploaded_dataset.data + if uploaded_dataset.type == 'composite': + # we need to init metadata before the job is dispatched + data.init_meta() + for meta_name, meta_value in uploaded_dataset.metadata.iteritems(): + setattr( data.metadata, meta_name, meta_value ) + data.flush() + json = dict( file_type = uploaded_dataset.file_type, + dataset_id = data.dataset.id, + dbkey = uploaded_dataset.dbkey, + type = uploaded_dataset.type, + metadata = uploaded_dataset.metadata, + primary_file = uploaded_dataset.primary_file, + extra_files_path = data.extra_files_path, + composite_file_paths = uploaded_dataset.composite_files, + composite_files = dict( [ ( k, v.__dict__ ) for k, v in data.datatype.get_composite_files( data ).items() ] ) ) + else: + try: + is_binary = uploaded_dataset.datatype.is_binary + except: + is_binary = None + json = dict( file_type = uploaded_dataset.file_type, + ext = uploaded_dataset.ext, + name = uploaded_dataset.name, + dataset_id = data.dataset.id, + dbkey = uploaded_dataset.dbkey, + type = uploaded_dataset.type, + is_binary = is_binary, + space_to_tab = uploaded_dataset.space_to_tab, + path = uploaded_dataset.path ) + json_file.write( to_json_string( json ) + '\n' ) json_file.close() - return ( json_file_path, data_list ) + return json_file_path def create_job( trans, params, tool, json_file_path, data_list, folder=None ): """ diff -r 389226e41780 -r 30a175ace572 lib/galaxy/web/controllers/library.py --- a/lib/galaxy/web/controllers/library.py Mon Sep 28 18:57:25 2009 -0400 +++ b/lib/galaxy/web/controllers/library.py Tue Sep 29 12:17:57 2009 -0400 @@ -114,8 +114,11 @@ messagetype='error' ) ) created_ldda_ids = params.get( 'created_ldda_ids', '' ) hidden_folder_ids = util.listify( util.restore_text( params.get( 'hidden_folder_ids', '' ) ) ) + if created_ldda_ids and not msg: + msg = "%d datasets are now uploading in the background to the library '%s' ( each is selected ). Please do not navigate away from Galaxy or use the browser's \"stop\" or \"reload\" buttons (on this tab) until the upload(s) change from the \"uploading\" state." % ( len( created_ldda_ids.split(',') ), library.name ) + messagetype = "info" return trans.fill_template( '/library/browse_library.mako', - library=trans.app.model.Library.get( id ), + library=library, created_ldda_ids=created_ldda_ids, hidden_folder_ids=hidden_folder_ids, default_action=params.get( 'default_action', None ), @@ -716,7 +719,7 @@ messagetype=messagetype ) if trans.app.security_agent.can_add_library_item( user, roles, folder ) or \ ( replace_dataset and trans.app.security_agent.can_modify_library_item( user, roles, replace_dataset ) ): - if params.get( 'runtool_btn', False ): + if params.get( 'runtool_btn', False ) or params.get( 'ajax_upload', False ): # See if we have any inherited templates, but do not inherit contents. info_association, inherited = folder.get_info_association( inherited=True ) if info_association: diff -r 389226e41780 -r 30a175ace572 lib/galaxy/web/controllers/library_admin.py --- a/lib/galaxy/web/controllers/library_admin.py Mon Sep 28 18:57:25 2009 -0400 +++ b/lib/galaxy/web/controllers/library_admin.py Tue Sep 29 12:17:57 2009 -0400 @@ -49,8 +49,11 @@ msg=util.sanitize_text( msg ), messagetype='error' ) ) created_ldda_ids = params.get( 'created_ldda_ids', '' ) + if created_ldda_ids and not msg: + msg = "%d datasets are now uploading in the background to the library '%s' ( each is selected ). Please do not navigate away from Galaxy or use the browser's \"stop\" or \"reload\" buttons (on this tab) until the upload(s) change from the \"uploading\" state." % ( len( created_ldda_ids.split(',') ), library.name ) + messagetype = "info" return trans.fill_template( '/admin/library/browse_library.mako', - library=trans.app.model.Library.get( id ), + library=library, deleted=deleted, created_ldda_ids=created_ldda_ids, forms=get_all_forms( trans, filter=dict(deleted=False) ), @@ -428,7 +431,7 @@ # The built-in 'id' is overwritten in lots of places as well ldatatypes = [ dtype_name for dtype_name, dtype_value in trans.app.datatypes_registry.datatypes_by_extension.iteritems() if dtype_value.allow_datatype_change ] ldatatypes.sort() - if params.get( 'runtool_btn', False ): + if params.get( 'runtool_btn', False ) or params.get( 'ajax_upload', False ): # See if we have any inherited templates, but do not inherit contents. info_association, inherited = folder.get_info_association( inherited=True ) if info_association: diff -r 389226e41780 -r 30a175ace572 lib/galaxy/web/controllers/library_dataset.py --- a/lib/galaxy/web/controllers/library_dataset.py Mon Sep 28 18:57:25 2009 -0400 +++ b/lib/galaxy/web/controllers/library_dataset.py Tue Sep 29 12:17:57 2009 -0400 @@ -32,7 +32,6 @@ #"force_history_refresh": force_history_refresh } return rval - @web.expose def upload_dataset( self, trans, controller, library_id, folder_id, replace_dataset=None, **kwd ): # Set up the traditional tool state/params tool_id = 'upload1' @@ -46,6 +45,7 @@ dataset_upload_inputs.append( input ) # Library-specific params params = util.Params( kwd ) # is this filetoolparam safe? + library_bunch = upload_common.handle_library_params( trans, params, folder_id, replace_dataset ) msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) server_dir = util.restore_text( params.get( 'server_dir', '' ) ) @@ -53,25 +53,8 @@ replace_id = replace_dataset.id else: replace_id = None - message = params.get( 'message', '' ) upload_option = params.get( 'upload_option', 'upload_file' ) err_redirect = False - # See if we have any template field contents - template_field_contents = [] - template_id = params.get( 'template_id', None ) - folder = trans.app.model.LibraryFolder.get( folder_id ) - # We are inheriting the folder's info_association, so we did not - # receive any inherited contents, but we may have redirected here - # after the user entered template contents ( due to errors ). - if template_id not in [ None, 'None' ]: - template = trans.app.model.FormDefinition.get( template_id ) - for field_index in range( len( template.fields ) ): - field_name = 'field_%i' % field_index - if params.get( field_name, False ): - field_value = util.restore_text( params.get( field_name, '' ) ) - template_field_contents.append( field_value ) - else: - template = None if upload_option == 'upload_directory': if server_dir in [ None, 'None', '' ]: err_redirect = True @@ -90,25 +73,18 @@ msg = 'Select a directory' else: msg = '"%s" is not defined in the Galaxy configuration file' % import_dir_desc - roles = [] - for role_id in util.listify( params.get( 'roles', [] ) ): - roles.append( trans.app.model.Role.get( role_id ) ) # Proceed with (mostly) regular upload processing - precreated_datasets = upload_common.get_precreated_datasets( trans, tool_params, trans.app.model.HistoryDatasetAssociation ) + precreated_datasets = upload_common.get_precreated_datasets( trans, tool_params, trans.app.model.LibraryDatasetDatasetAssociation, controller=controller ) if upload_option == 'upload_file': tool_params = upload_common.persist_uploads( tool_params ) - json_file_path, data_list = upload_common.create_paramfile( trans, tool_params, precreated_datasets, dataset_upload_inputs, replace_dataset, folder, template, template_field_contents, roles, message ) + uploaded_datasets = upload_common.get_uploaded_datasets( trans, tool_params, precreated_datasets, dataset_upload_inputs, library_bunch=library_bunch ) elif upload_option == 'upload_directory': - json_file_path, data_list = self.create_server_dir_paramfile( trans, params, full_dir, import_dir_desc, folder, template, template_field_contents, roles, message, err_redirect, msg ) + uploaded_datasets = self.get_server_dir_uploaded_datasets( trans, params, full_dir, import_dir_desc, library_bunch, err_redirect, msg ) upload_common.cleanup_unused_precreated_datasets( precreated_datasets ) - if upload_option == 'upload_file' and not data_list: + if upload_option == 'upload_file' and not uploaded_datasets: msg = 'Select a file, enter a URL or enter text' err_redirect = True if err_redirect: - try: - os.remove( json_file_path ) - except: - pass trans.response.send_redirect( web.url_for( controller=controller, action='library_dataset_dataset_association', library_id=library_id, @@ -117,12 +93,10 @@ upload_option=upload_option, msg=util.sanitize_text( msg ), messagetype='error' ) ) - return upload_common.create_job( trans, tool_params, tool, json_file_path, data_list, folder=folder ) - def create_server_dir_paramfile( self, trans, params, full_dir, import_dir_desc, folder, template, - template_field_contents, roles, message, err_redirect, msg ): - """ - Create JSON param file for the upload tool when using the server_dir upload. - """ + json_file_path = upload_common.create_paramfile( uploaded_datasets ) + data_list = [ ud.data for ud in uploaded_datasets ] + return upload_common.create_job( trans, tool_params, tool, json_file_path, data_list, folder=library_bunch.folder ) + def get_server_dir_uploaded_datasets( self, trans, params, full_dir, import_dir_desc, library_bunch, err_redirect, msg ): files = [] try: for entry in os.listdir( full_dir ): @@ -132,34 +106,24 @@ except Exception, e: msg = "Unable to get file list for configured %s, error: %s" % ( import_dir_desc, str( e ) ) err_redirect = True - return ( None, None ) + return None if not files: msg = "The directory '%s' contains no valid files" % full_dir err_redirect = True - return ( None, None ) - data_list = [] - json_file = tempfile.mkstemp() - json_file_path = json_file[1] - json_file = os.fdopen( json_file[0], 'w' ) + return None + uploaded_datasets = [] for file in files: - full_file = os.path.join( full_dir, file ) - if not os.path.isfile( full_file ): + library_bunch.replace_dataset = None + uploaded_dataset = util.bunch.Bunch() + uploaded_dataset.path = os.path.join( full_dir, file ) + if not os.path.isfile( uploaded_dataset.path ): continue - uploaded_dataset = util.bunch.Bunch() + uploaded_dataset.type = 'server_dir' uploaded_dataset.name = file + uploaded_dataset.ext = None uploaded_dataset.file_type = params.file_type uploaded_dataset.dbkey = params.dbkey - data = upload_common.new_library_upload( trans, uploaded_dataset, None, folder, template, template_field_contents, roles, message ) - json = dict( file_type = uploaded_dataset.file_type, - ext = None, - name = uploaded_dataset.name, - dataset_id = data.dataset.id, - dbkey = uploaded_dataset.dbkey, - type = 'server_dir', - is_binary = None, - space_to_tab = params.space_to_tab, - path = full_file ) - json_file.write( to_json_string( json ) + '\n' ) - data_list.append( data ) - json_file.close() - return ( json_file_path, data_list ) + uploaded_dataset.space_to_tab = params.space_to_tab + uploaded_dataset.data = upload_common.new_upload( trans, uploaded_dataset, library_bunch ) + uploaded_datasets.append( uploaded_dataset ) + return uploaded_datasets diff -r 389226e41780 -r 30a175ace572 lib/galaxy/web/controllers/tool_runner.py --- a/lib/galaxy/web/controllers/tool_runner.py Mon Sep 28 18:57:25 2009 -0400 +++ b/lib/galaxy/web/controllers/tool_runner.py Tue Sep 29 12:17:57 2009 -0400 @@ -6,6 +6,7 @@ from galaxy.util.bunch import Bunch from galaxy.tools import DefaultToolState from galaxy.tools.parameters.basic import UnvalidatedValue +from galaxy.tools.actions import upload_common import logging log = logging.getLogger( __name__ ) @@ -137,20 +138,24 @@ Precreate datasets for asynchronous uploading. """ permissions = trans.app.security_agent.history_get_default_permissions( trans.history ) - def create_dataset( name, history ): - data = trans.app.model.HistoryDatasetAssociation( create_dataset = True ) - data.name = name - data.state = data.states.UPLOAD - data.history = history - data.flush() - history.add_dataset( data ) - trans.app.security_agent.set_all_dataset_permissions( data.dataset, permissions ) - return data + def create_dataset( name ): + ud = Bunch( name=name, file_type=None, dbkey=None ) + # Okay, time to make this crap actually use the upload_common functions, which means making them get called from outside the json_paramfile method. + if nonfile_params.get( 'folder_id', False ): + replace_id = nonfile_params.get( 'replace_id', None ) + if replace_id not in [ None, 'None' ]: + replace_dataset = trans.app.model.LibraryDataset.get( int( replace_id ) ) + else: + replace_dataset = None + library_bunch = upload_common.handle_library_params( trans, nonfile_params, nonfile_params.folder_id, replace_dataset ) + else: + library_bunch = None + return upload_common.new_upload( trans, ud, library_bunch=library_bunch, state=trans.app.model.HistoryDatasetAssociation.states.UPLOAD ) tool = self.get_toolbox().tools_by_id.get( tool_id, None ) if not tool: return False # bad tool_id - #params = util.Params( kwd, sanitize=tool.options.sanitize, tool=tool ) - if "tool_state" in kwd: + nonfile_params = util.Params( kwd, sanitize=tool.options.sanitize, tool=tool ) + if kwd.get( 'tool_state', None ) not in ( None, 'None' ): encoded_state = util.string_to_object( kwd["tool_state"] ) tool_state = DefaultToolState() tool_state.decode( encoded_state, tool, trans.app ) @@ -167,7 +172,7 @@ d_type = dataset_upload_input.get_datatype( trans, kwd ) if d_type.composite_type is not None: - datasets.append( create_dataset( 'Uploaded Composite Dataset (%s)' % dataset_upload_input.get_datatype_ext( trans, kwd ), trans.history ) ) + datasets.append( create_dataset( 'Uploaded Composite Dataset (%s)' % dataset_upload_input.get_datatype_ext( trans, kwd ) ) ) else: params = Bunch( ** tool_state.inputs[dataset_upload_input.name][0] ) if params.file_data not in [ None, "" ]: @@ -176,7 +181,7 @@ name = name.rsplit('/',1)[1] if name.count('\\'): name = name.rsplit('\\',1)[1] - datasets.append( create_dataset( name, trans.history ) ) + datasets.append( create_dataset( name ) ) if params.url_paste not in [ None, "" ]: url_paste = params.url_paste.replace( '\r', '' ).split( '\n' ) url = False @@ -186,13 +191,13 @@ continue elif line.lower().startswith( 'http://' ) or line.lower().startswith( 'ftp://' ): url = True - datasets.append( create_dataset( line, trans.history ) ) + datasets.append( create_dataset( line ) ) else: if url: continue # non-url when we've already processed some urls else: # pasted data - datasets.append( create_dataset( 'Pasted Entry', trans.history ) ) + datasets.append( create_dataset( 'Pasted Entry' ) ) break if datasets: trans.model.flush() diff -r 389226e41780 -r 30a175ace572 static/june_2007_style/blue/library.css --- a/static/june_2007_style/blue/library.css Mon Sep 28 18:57:25 2009 -0400 +++ b/static/june_2007_style/blue/library.css Tue Sep 29 12:17:57 2009 -0400 @@ -18,3 +18,4 @@ .libraryItem-error{margin-right:2px;padding:0 2px 0 2px;border:1px solid #AA6666;background:#FFCCCC;} .libraryItem-queued{margin-right:2px;padding:0 2px 0 2px;border:1px solid #888888;background:#EEEEEE;} .libraryItem-running{margin-right:2px;padding:0 2px 0 2px;border:1px solid #AAAA66;background:#FFFFCC;} +.libraryItem-upload{margin-right:2px;padding:0 2px 0 2px;border:1px solid #6666AA;background:#CCCCFF;} diff -r 389226e41780 -r 30a175ace572 static/june_2007_style/library.css.tmpl --- a/static/june_2007_style/library.css.tmpl Mon Sep 28 18:57:25 2009 -0400 +++ b/static/june_2007_style/library.css.tmpl Tue Sep 29 12:17:57 2009 -0400 @@ -109,3 +109,9 @@ background: $history_running_bg; } +.libraryItem-upload { + margin-right: 2px; + padding: 0 2px 0 2px; + border: 1px solid $history_upload_border; + background: $history_upload_bg; +} diff -r 389226e41780 -r 30a175ace572 templates/base_panels.mako --- a/templates/base_panels.mako Mon Sep 28 18:57:25 2009 -0400 +++ b/templates/base_panels.mako Tue Sep 29 12:17:57 2009 -0400 @@ -70,12 +70,28 @@ ## Handle AJAX (actually hidden iframe) upload tool <![if !IE]> <script type="text/javascript"> + var upload_form_error = function( msg ) { + if ( ! $("iframe#galaxy_main").contents().find("body").find("div[name='upload_error']").size() ) { + $("iframe#galaxy_main").contents().find("body").prepend( '<div class="errormessage" name="upload_error">' + msg + '</div><p/>' ); + } else { + $("iframe#galaxy_main").contents().find("body").find("div[name='upload_error']").text( msg ); + } + } jQuery( function() { $("iframe#galaxy_main").load( function() { $(this).contents().find("form").each( function() { if ( $(this).find("input[galaxy-ajax-upload]").length > 0 ){ $(this).submit( function() { - var error_set = false; + // Only bother using a hidden iframe if there's a file (e.g. big data) upload + var file_upload = false; + $(this).find("input[galaxy-ajax-upload]").each( function() { + if ( $(this).val() != '' ) { + file_upload = true; + } + }); + if ( ! file_upload ) { + return true; + } // Make a synchronous request to create the datasets first var async_datasets; $.ajax( { @@ -87,10 +103,7 @@ success: function( d, s ) { async_datasets = d.join() } } ); if (async_datasets == '') { - if (! error_set) { - $("iframe#galaxy_main").contents().find("body").prepend( '<div class="errormessage">No data was entered in the upload form. You may choose to upload a file, paste some data directly in the data box, or enter URL(s) to fetch from.</div><p/>' ); - error_set = true; - } + upload_form_error( 'No data was entered in the upload form. You may choose to upload a file, paste some data directly in the data box, or enter URL(s) to fetch from.' ); return false; } else { $(this).find("input[name=async_datasets]").val( async_datasets ); @@ -98,7 +111,16 @@ } // iframe submit is required for nginx (otherwise the encoding is wrong) $(this).ajaxSubmit( { iframe: true } ); - $("iframe#galaxy_main").attr("src","${h.url_for(controller='tool_runner', action='upload_async_message')}"); + if ( $(this).find("input[name='folder_id']").val() != undefined ) { + var library_id = $(this).find("input[name='library_id']").val(); + if ( location.pathname.indexOf( 'library_admin' ) ) { + $("iframe#galaxy_main").attr("src","${h.url_for(controller='library_admin', action='browse_library' )}?id=" + library_id + "&created_ldda_ids=" + async_datasets); + } else { + $("iframe#galaxy_main").attr("src","${h.url_for(controller='library', action='browse_library' )}?id=" + library_id + "&created_ldda_ids=" + async_datasets); + } + } else { + $("iframe#galaxy_main").attr("src","${h.url_for(controller='tool_runner', action='upload_async_message')}"); + } return false; }); } diff -r 389226e41780 -r 30a175ace572 templates/library/library_dataset_common.mako --- a/templates/library/library_dataset_common.mako Mon Sep 28 18:57:25 2009 -0400 +++ b/templates/library/library_dataset_common.mako Tue Sep 29 12:17:57 2009 -0400 @@ -8,9 +8,10 @@ <div class="toolFormTitle">Upload a directory of files</div> %endif <div class="toolFormBody"> - <form name="upload_library_dataset" action="${h.url_for( controller=controller, action='library_dataset_dataset_association', library_id=library_id )}" enctype="multipart/form-data" method="post"> - <input type="hidden" name="tool_id" value="upload_library_dataset"/> + <form name="upload_library_dataset" action="${h.url_for( controller=controller, action='library_dataset_dataset_association' )}" enctype="multipart/form-data" method="post"> + <input type="hidden" name="tool_id" value="upload1"/> <input type="hidden" name="tool_state" value="None"/> + <input type="hidden" name="library_id" value="${library_id}"/> <input type="hidden" name="folder_id" value="${folder_id}"/> <input type="hidden" name="upload_option" value="${upload_option}"/> %if replace_dataset not in [ None, 'None' ]: @@ -40,8 +41,7 @@ <div class="form-row"> <label>File:</label> <div class="form-row-input"> - ##<input type="file" name="files_0|file_data" galaxy-ajax-upload="true"/> - <input type="file" name="files_0|file_data"/> + <input type="file" name="files_0|file_data" galaxy-ajax-upload="true"/> </div> <div style="clear: both"></div> </div> diff -r 389226e41780 -r 30a175ace572 templates/library/library_item_info.mako --- a/templates/library/library_item_info.mako Mon Sep 28 18:57:25 2009 -0400 +++ b/templates/library/library_item_info.mako Tue Sep 29 12:17:57 2009 -0400 @@ -5,6 +5,8 @@ <div class="libraryItem-${ldda.state}">This job is queued</div> %elif ldda.state == 'running': <div class="libraryItem-${ldda.state}">This job is running</div> + %elif ldda.state == 'upload': + <div class="libraryItem-${ldda.state}">This dataset is uploading</div> %else: ${ldda.message} %endif

1 0

[hg] galaxy 2789: typo fixes for tools in folders A-M
by Nate Coraor 02 Oct '09

02 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/d669408018a1 changeset: 2789:d669408018a1 user: Kanwei Li <kanwei(a)gmail.com> date: Sun Sep 27 23:11:43 2009 -0400 description: typo fixes for tools in folders A-M 38 file(s) affected in this change: templates/base_panels.mako tools/annotation_profiler/annotation_profiler.xml tools/data_source/encode_import_all_latest_datasets.xml tools/data_source/upload.xml tools/extract/extract_genomic_dna.xml tools/fastx_toolkit/fasta_formatter.xml tools/fastx_toolkit/fastq_quality_converter.xml tools/fastx_toolkit/fastx_barcode_splitter.xml tools/fastx_toolkit/fastx_clipper.xml tools/fastx_toolkit/fastx_collapser.xml tools/fastx_toolkit/fastx_quality_statistics.xml tools/fastx_toolkit/fastx_renamer.xml tools/filters/axt_to_concat_fasta.xml tools/filters/axt_to_fasta.xml tools/filters/axt_to_lav.xml tools/filters/compare.xml tools/filters/cutWrapper.xml tools/filters/grep.xml tools/filters/joiner.xml tools/filters/lav_to_bed.xml tools/filters/pasteWrapper.xml tools/filters/remove_beginning.xml tools/hyphy/hyphy_dnds_wrapper.xml tools/hyphy/hyphy_nj_tree_wrapper.xml tools/maf/genebed_maf_to_fasta.xml tools/maf/interval_maf_to_merged_fasta.xml tools/maf/maf_to_bed.xml tools/maf/maf_to_fasta.xml tools/maf/maf_to_interval.xml tools/metag_tools/blat_wrapper.xml tools/metag_tools/convert_SOLiD_color2nuc.xml tools/metag_tools/mapping_to_ucsc.xml tools/metag_tools/megablast_xml_parser.xml tools/metag_tools/short_reads_figure_high_quality_length.xml tools/metag_tools/short_reads_figure_score.xml tools/metag_tools/short_reads_trim_seq.xml tools/metag_tools/shrimp_color_wrapper.xml tools/metag_tools/shrimp_wrapper.xml diffs (698 lines): diff -r f7459ad62be9 -r d669408018a1 templates/base_panels.mako --- a/templates/base_panels.mako Sat Sep 26 18:05:36 2009 -0400 +++ b/templates/base_panels.mako Sun Sep 27 23:11:43 2009 -0400 @@ -283,7 +283,7 @@ </head> <body scroll="no" class="${self.body_class}"> - <div id="everything" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%; min-width: 960px;"> + <div id="everything" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%; min-width: 600px;"> ## Background displays first <div id="background"></div> ## Layer iframes over backgrounds diff -r f7459ad62be9 -r d669408018a1 tools/annotation_profiler/annotation_profiler.xml --- a/tools/annotation_profiler/annotation_profiler.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/annotation_profiler/annotation_profiler.xml Sun Sep 27 23:11:43 2009 -0400 @@ -43,9 +43,9 @@ Takes an input set of intervals and for each interval determines the base coverage of the interval by a set of features (tables) available from UCSC. -By default, this tool will check the coverage of your intervals against all available features; you may, however, choose to select only those tables that you want to include. Selecting a section heading will effectively cause all of it's children to be selected. +By default, this tool will check the coverage of your intervals against all available features; you may, however, choose to select only those tables that you want to include. Selecting a section heading will effectively cause all of its children to be selected. -You may alternatively choose to recieve a summary across all of the intervals that you provide. +You may alternatively choose to receive a summary across all of the intervals that you provide. ----- @@ -118,14 +118,14 @@ allIntervalCount is the number of provided intervals allIntervalSize is the sum of the lengths of the provided interval file allCoverage is the sum of the coverage for each provided interval - allTableRegionsOverlaped is the sum of the number of regions of the table (non-unique) that were overlaped for each interval - allIntervalsOverlapingTable is the number of provided intervals which overlap the table + allTableRegionsOverlapped is the sum of the number of regions of the table (non-unique) that were overlapped for each interval + allIntervalsOverlappingTable is the number of provided intervals which overlap the table nrIntervalCount is the number of non-redundant intervals nrIntervalSize is the sum of the lengths of non-redundant intervals nrCoverage is the sum of the coverage of non-redundant intervals - nrTableRegionsOverlaped is the number of regions of the table (unique) that were overlaped by the non-redundant intervals - nrIntervalsOverlapingTable is the number of non-redundant intervals which overlap the table + nrTableRegionsOverlapped is the number of regions of the table (unique) that were overlapped by the non-redundant intervals + nrIntervalsOverlappingTable is the number of non-redundant intervals which overlap the table .. class:: infomark diff -r f7459ad62be9 -r d669408018a1 tools/data_source/encode_import_all_latest_datasets.xml --- a/tools/data_source/encode_import_all_latest_datasets.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/data_source/encode_import_all_latest_datasets.xml Sun Sep 27 23:11:43 2009 -0400 @@ -46,7 +46,7 @@ *[gencode_partitioned]* means that the dataset was partitioned according to the protocol below: -A partition scheme has been defined that is similar to what has previously been done with TARs/TRANSFRAGs such that any feature can be cla ssified as falling into one of the following 6 categories: +A partition scheme has been defined that is similar to what has previously been done with TARs/TRANSFRAGs such that any feature can be classified as falling into one of the following 6 categories: 1. **Coding** -- coding exons defined from the GENCODE experimentally verified coding set (coding in any transcript) 2. **5UTR** -- 5' UTR exons defined from the GENCODE experimentally verified coding set (5' UTR in some transcript but never coding in any other) 3. **3UTR** -- 3' UTR exons defined from the GENCODE experimentally verified coding set (3' UTR in some transcript but never coding in any other) @@ -63,4 +63,4 @@ </help> -</tool> +</tool> diff -r f7459ad62be9 -r d669408018a1 tools/data_source/upload.xml --- a/tools/data_source/upload.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/data_source/upload.xml Sun Sep 27 23:11:43 2009 -0400 @@ -94,7 +94,7 @@ **Fasta** -A sequence in FASTA format consists of a single-line description, followed by lines of sequence data. The first character of the description line is a greater-than (">") symbol in the first column. All lines should be shorter than 80 charcters:: +A sequence in FASTA format consists of a single-line description, followed by lines of sequence data. The first character of the description line is a greater-than (">") symbol in the first column. All lines should be shorter than 80 characters:: >sequence1 atgcgtttgcgtgc @@ -195,7 +195,7 @@ **Wig** -The wiggle format is line-oriented. Wiggle data is preceeded by a track definition line, which adds a number of options for controlling the default display of this track. +The wiggle format is line-oriented. Wiggle data is preceded by a track definition line, which adds a number of options for controlling the default display of this track. ----- diff -r f7459ad62be9 -r d669408018a1 tools/extract/extract_genomic_dna.xml --- a/tools/extract/extract_genomic_dna.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/extract/extract_genomic_dna.xml Sun Sep 27 23:11:43 2009 -0400 @@ -55,7 +55,7 @@ .. class:: infomark - **Extract genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes** previously were achieved by two seperate tools. + **Extract genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes** previously were achieved by two separate tools. ----- diff -r f7459ad62be9 -r d669408018a1 tools/fastx_toolkit/fasta_formatter.xml --- a/tools/fastx_toolkit/fasta_formatter.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/fastx_toolkit/fasta_formatter.xml Sun Sep 27 23:11:43 2009 -0400 @@ -13,7 +13,7 @@ <inputs> <param format="fasta" name="input" type="data" label="Library to re-format" /> - <param name="width" type="integer" value="0" label="New width for nucleotides strings" help="Use 0 for single line outout." /> + <param name="width" type="integer" value="0" label="New width for nucleotides strings" help="Use 0 for single line out." /> </inputs> <tests> diff -r f7459ad62be9 -r d669408018a1 tools/fastx_toolkit/fastq_quality_converter.xml --- a/tools/fastx_toolkit/fastq_quality_converter.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/fastx_toolkit/fastq_quality_converter.xml Sun Sep 27 23:11:43 2009 -0400 @@ -53,7 +53,7 @@ **What it does** -Converts a solexa FASTQ file to/from numeric or ASCII quality format. +Converts a Solexa FASTQ file to/from numeric or ASCII quality format. .. class:: warningmark diff -r f7459ad62be9 -r d669408018a1 tools/fastx_toolkit/fastx_barcode_splitter.xml --- a/tools/fastx_toolkit/fastx_barcode_splitter.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/fastx_toolkit/fastx_barcode_splitter.xml Sun Sep 27 23:11:43 2009 -0400 @@ -36,7 +36,7 @@ **What it does** -This tool splits a solexa library (FASTQ file) or a regular FASTA file to several files, using barcodes as the split criteria. +This tool splits a Solexa library (FASTQ file) or a regular FASTA file into several files, using barcodes as the split criteria. -------- diff -r f7459ad62be9 -r d669408018a1 tools/fastx_toolkit/fastx_clipper.xml --- a/tools/fastx_toolkit/fastx_clipper.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/fastx_toolkit/fastx_clipper.xml Sun Sep 27 23:11:43 2009 -0400 @@ -42,8 +42,8 @@ </param> <param name="DISCARD_OPTIONS" type="select" label="Output options"> - <option value="-c">Output only clipped seqeunces (i.e. sequences which contained the adapter)</option> - <option value="-C">Output only non-clipped seqeunces (i.e. sequences which did not contained the adapter)</option> + <option value="-c">Output only clipped sequences (i.e. sequences which contained the adapter)</option> + <option value="-C">Output only non-clipped sequences (i.e. sequences which did not contained the adapter)</option> <option value="">Output both clipped and non-clipped sequences</option> </param> diff -r f7459ad62be9 -r d669408018a1 tools/fastx_toolkit/fastx_collapser.xml --- a/tools/fastx_toolkit/fastx_collapser.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/fastx_toolkit/fastx_collapser.xml Sun Sep 27 23:11:43 2009 -0400 @@ -63,7 +63,7 @@ Original Sequence Names / Lane descriptions (e.g. "CSHL_2_FC0042AGLLOO_1_1_742_502") are discarded. -The output seqeunce name is composed of two numbers: the first is the sequence's number, the second is the multiplicity value. +The output sequence name is composed of two numbers: the first is the sequence's number, the second is the multiplicity value. The following output:: diff -r f7459ad62be9 -r d669408018a1 tools/fastx_toolkit/fastx_quality_statistics.xml --- a/tools/fastx_toolkit/fastx_quality_statistics.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/fastx_toolkit/fastx_quality_statistics.xml Sun Sep 27 23:11:43 2009 -0400 @@ -36,7 +36,7 @@ **The output file will contain the following fields:** -* column = column number (1 to 36 for a 36-cycles read solexa file) +* column = column number (1 to 36 for a 36-cycles read Solexa file) * count = number of bases found in this column. * min = Lowest quality score value found in this column. * max = Highest quality score value found in this column. diff -r f7459ad62be9 -r d669408018a1 tools/fastx_toolkit/fastx_renamer.xml --- a/tools/fastx_toolkit/fastx_renamer.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/fastx_toolkit/fastx_renamer.xml Sun Sep 27 23:11:43 2009 -0400 @@ -23,7 +23,7 @@ .. class:: infomark -Use this tool at the beginning of your workflow, as a way to keep the original sequence (before trimming,clipping,barcode-removal, etc). +Use this tool at the beginning of your workflow, as a way to keep the original sequence (before trimming, clipping, barcode-removal, etc). -------- diff -r f7459ad62be9 -r d669408018a1 tools/filters/axt_to_concat_fasta.xml --- a/tools/filters/axt_to_concat_fasta.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/filters/axt_to_concat_fasta.xml Sun Sep 27 23:11:43 2009 -0400 @@ -1,5 +1,5 @@ <tool id="axt_to_concat_fasta" name="AXT to concatenated FASTA"> - <description>Converts an AXT formated file to a concatenated FASTA alignment</description> + <description>Converts an AXT formatted file to a concatenated FASTA alignment</description> <command interpreter="python">axt_to_concat_fasta.py $dbkey_1 $dbkey_2 < $axt_input > $out_file1</command> <inputs> <param format="axt" name="axt_input" type="data" label="AXT file"/> @@ -27,7 +27,7 @@ **Syntax** -This tool converts an AXT formated file to the FASTA format, and concatenates the results in the same build. +This tool converts an AXT formatted file to the FASTA format, and concatenates the results in the same build. - **AXT format** The alignments are produced from Blastz, an alignment tool available from Webb Miller's lab at Penn State University. The lav format Blastz output, which does not include the sequence, was converted to AXT format with lavToAxt. Each alignment block in an AXT file contains three lines: a summary line and 2 sequence lines. Blocks are separated from one another by blank lines. diff -r f7459ad62be9 -r d669408018a1 tools/filters/axt_to_fasta.xml --- a/tools/filters/axt_to_fasta.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/filters/axt_to_fasta.xml Sun Sep 27 23:11:43 2009 -0400 @@ -1,5 +1,5 @@ <tool id="axt_to_fasta" name="AXT to FASTA"> - <description>Converts an AXT formated file to FASTA format</description> + <description>Converts an AXT formatted file to FASTA format</description> <command interpreter="python">axt_to_fasta.py $dbkey_1 $dbkey_2 < $axt_input > $out_file1</command> <inputs> <param format="axt" name="axt_input" type="data" label="AXT file"/> @@ -28,7 +28,7 @@ **Syntax** -This tool converts an AXT formated file to the FASTA format. +This tool converts an AXT formatted file to the FASTA format. - **AXT format** The alignments are produced from Blastz, an alignment tool available from Webb Miller's lab at Penn State University. The lav format Blastz output, which does not include the sequence, was converted to AXT format with lavToAxt. Each alignment block in an AXT file contains three lines: a summary line and 2 sequence lines. Blocks are separated from one another by blank lines. diff -r f7459ad62be9 -r d669408018a1 tools/filters/axt_to_lav.xml --- a/tools/filters/axt_to_lav.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/filters/axt_to_lav.xml Sun Sep 27 23:11:43 2009 -0400 @@ -1,5 +1,5 @@ <tool id="axt_to_lav_1" name="AXT to LAV"> - <description>Converts an AXT formated file to LAV format</description> + <description>Converts an AXT formatted file to LAV format</description> <command interpreter="python">axt_to_lav.py /depot/data2/galaxy/$dbkey_1/seq/%s.nib:$dbkey_1:${GALAXY_DATA_INDEX_DIR}/shared/ucsc/chrom/${dbkey_1}.len /depot/data2/galaxy/$dbkey_2/seq/%s.nib:$dbkey_2:${GALAXY_DATA_INDEX_DIR}/shared/ucsc/chrom/${dbkey_2}.len $align_input $lav_file $seq_file1 $seq_file2</command> <inputs> <param name="align_input" type="data" format="axt" label="Alignment File" optional="False"/> @@ -22,7 +22,7 @@ **Syntax** -This tool converts an AXT formated file to the LAV format. +This tool converts an AXT formatted file to the LAV format. - **AXT format** The alignments are produced from Blastz, an alignment tool available from Webb Miller's lab at Penn State University. The lav format Blastz output, which does not include the sequence, was converted to AXT format with lavToAxt. Each alignment block in an AXT file contains three lines: a summary line and 2 sequence lines. Blocks are separated from one another by blank lines. diff -r f7459ad62be9 -r d669408018a1 tools/filters/compare.xml --- a/tools/filters/compare.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/filters/compare.xml Sun Sep 27 23:11:43 2009 -0400 @@ -52,7 +52,7 @@ and this is **Second query**:: - geneA tumor-supressor + geneA tumor-suppressor geneB Foxp2 geneC Gnas1 geneE INK4a diff -r f7459ad62be9 -r d669408018a1 tools/filters/cutWrapper.xml --- a/tools/filters/cutWrapper.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/filters/cutWrapper.xml Sun Sep 27 23:11:43 2009 -0400 @@ -33,7 +33,7 @@ .. class:: infomark -The output of this tool is always in tabular format (e.g., if your original delimeter was comma, it will be replaced with tab). For example: +The output of this tool is always in tabular format (e.g., if your original delimiters are commas, they will be replaced with tabs). For example: Cutting columns 1 and 3 from:: diff -r f7459ad62be9 -r d669408018a1 tools/filters/grep.xml --- a/tools/filters/grep.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/filters/grep.xml Sun Sep 27 23:11:43 2009 -0400 @@ -30,7 +30,7 @@ **Syntax** -The select tool searches the data for lines containing or not containing a match to the given pattern. Regular Expression is introduced in this tool. A Regular Expression is a pattern descibing a certain amount of text. +The select tool searches the data for lines containing or not containing a match to the given pattern. Regular Expression is introduced in this tool. A Regular Expression is a pattern describing a certain amount of text. - **( ) { } [ ] . * ? + \ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for. - **\\A** matches the beginning of a string(but not an internal line). @@ -46,7 +46,7 @@ - **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern. - **{n}** The preceding item is matched exactly n times. - - **{n,}** The preceding item ismatched n or more times. + - **{n,}** The preceding item is matched n or more times. - **{n,m}** The preceding item is matched at least n times but not more than m times. - **[** ... **]** creates a character class. Within the brackets, single characters can be placed. A dash (-) may be used to indicate a range such as **a-z**. @@ -64,9 +64,9 @@ **Example** -- **^chr([0-9A-Za-z])+** would match lines that begin with chromsomes, such as lines in a BED format file. +- **^chr([0-9A-Za-z])+** would match lines that begin with chromosomes, such as lines in a BED format file. - **(ACGT){1,5}** would match at least 1 "ACGT" and at most 5 "ACGT" consecutively. -- **([^,][0-9]{1,3})(,[0-9]{3})\*** would match a large integer that is properly seperated with commas such as 23,078,651. +- **([^,][0-9]{1,3})(,[0-9]{3})\*** would match a large integer that is properly separated with commas such as 23,078,651. - **(abc)|(def)** would match either "abc" or "def". - **^\\W+#** would match any line that is a comment. </help> diff -r f7459ad62be9 -r d669408018a1 tools/filters/joiner.xml --- a/tools/filters/joiner.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/filters/joiner.xml Sun Sep 27 23:11:43 2009 -0400 @@ -166,12 +166,12 @@ Joining the 4th column of Query1 with the 1st column of Query2 will yield:: - chr1 10 20 geneA geneA tumor-supressor + chr1 10 20 geneA geneA tumor-suppressor chr1 50 80 geneB geneB Foxp2 Joining the 4th column of Query1 with the 1st column of Query2, while keeping all lines from Query1, will yield:: - chr1 10 20 geneA geneA tumor-supressor + chr1 10 20 geneA geneA tumor-suppressor chr1 50 80 geneB geneB Foxp2 chr5 10 40 geneL diff -r f7459ad62be9 -r d669408018a1 tools/filters/lav_to_bed.xml --- a/tools/filters/lav_to_bed.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/filters/lav_to_bed.xml Sun Sep 27 23:11:43 2009 -0400 @@ -1,5 +1,5 @@ <tool id="lav_to_bed1" name="LAV to BED"> - <description>Converts a LAV formated file to BED format</description> + <description>Converts a LAV formatted file to BED format</description> <command interpreter="python">lav_to_bed.py $lav_file $bed_file1 $bed_file2</command> <inputs> <param name="lav_file" type="data" format="lav" label="LAV File" optional="False"/> @@ -19,7 +19,7 @@ **Syntax** -This tool converts a LAV formated file to the BED format. +This tool converts a LAV formatted file to the BED format. - **LAV format** LAV is an alignment format developed by Webb Miller's group at Penn State University. It is the primary output format for BLASTZ. @@ -54,7 +54,7 @@ } #:eof -- To two BED formated files:: +- To two BED formatted files:: chr19 3001011 3001075 hg16_0 0 + chr19 3008278 3008357 hg16_1 0 + diff -r f7459ad62be9 -r d669408018a1 tools/filters/pasteWrapper.xml --- a/tools/filters/pasteWrapper.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/filters/pasteWrapper.xml Sun Sep 27 23:11:43 2009 -0400 @@ -33,7 +33,7 @@ .. class:: infomark -Paste preserves column assignments of the first dataset +Paste preserves column assignments of the first dataset. ----- diff -r f7459ad62be9 -r d669408018a1 tools/filters/remove_beginning.xml --- a/tools/filters/remove_beginning.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/filters/remove_beginning.xml Sun Sep 27 23:11:43 2009 -0400 @@ -19,7 +19,7 @@ **What it does** -This tool removes specified number of lines from the beginning of a dataset +This tool removes a specified number of lines from the beginning of a dataset. ----- diff -r f7459ad62be9 -r d669408018a1 tools/hyphy/hyphy_dnds_wrapper.xml --- a/tools/hyphy/hyphy_dnds_wrapper.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/hyphy/hyphy_dnds_wrapper.xml Sun Sep 27 23:11:43 2009 -0400 @@ -47,7 +47,7 @@ ----- -For the tree definition, you only need to specify the species build names. For example, you could use the tree *((hg17,panTro1),(mm5,rn3),canFam1)*, if your FASTA file looks like the example below. You may also use **Neighbor Joining Tree Builder** tool to obtain the tree definition:: +For the tree definition, you only need to specify the species build names. For example, you could use the tree *(hg17,panTro1),(mm5,rn3),canFam1)*, if your FASTA file looks like the example below. You may also use **Neighbor Joining Tree Builder** tool to obtain the tree definition:: >hg17.chr7(+):26907301-26907310|hg17_0 GTGGGAGGT diff -r f7459ad62be9 -r d669408018a1 tools/hyphy/hyphy_nj_tree_wrapper.xml --- a/tools/hyphy/hyphy_nj_tree_wrapper.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/hyphy/hyphy_nj_tree_wrapper.xml Sun Sep 27 23:11:43 2009 -0400 @@ -16,7 +16,7 @@ <option value="K2P">Kimura 2 parameter</option> <option value="JC69">Jukes-Cantor</option>  -  +    </param> diff -r f7459ad62be9 -r d669408018a1 tools/maf/genebed_maf_to_fasta.xml --- a/tools/maf/genebed_maf_to_fasta.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/maf/genebed_maf_to_fasta.xml Sun Sep 27 23:11:43 2009 -0400 @@ -48,10 +48,10 @@ </param> </when> </conditional> - <param name="overwrite_with_gaps" type="select" label="Split into Gapless MAF blocks" help="When set to Yes, blocks are divided around gaps appearing in any species. This will prevent gaps occuring in the interior of the sequence for an aligning species from overwriting a nucleotide found for the same position in a lower-scoring block."> + <param name="overwrite_with_gaps" type="select" label="Split into Gapless MAF blocks" help="When set to Yes, blocks are divided around gaps appearing in any species. This will prevent gaps occurring in the interior of the sequence for an aligning species from overwriting a nucleotide found for the same position in a lower-scoring block."> <option value="True" selected="true">No</option> <option value="False">Yes</option> - </param> + </param> </inputs> <outputs> <data format="fasta" name="out_file1" /> @@ -61,7 +61,7 @@ <param name="input1" value="8.bed"/> <param name="maf_source" value="cached"/>in aligning species <param name="maf_identifier" value="8_WAY_MULTIZ_hg17"/> - <param name="species" value="canFam1,hg17,mm5,panTro1,rn3"/> + <param name="species" value="canFam1,hg17,mm5,panTro1,rn3"/> <param name="overwrite_with_gaps" value="True"/> <output name="out_file1" file="gene_bed_maf_to_fasta_out.fasta" /> </test> @@ -69,7 +69,7 @@ <param name="input1" value="8.bed"/> <param name="maf_source" value="user"/> <param name="maf_file" value="4.maf"/> - <param name="species" value="hg17,panTro1"/> + <param name="species" value="hg17,panTro1"/> <param name="overwrite_with_gaps" value="True"/> <output name="out_file1" file="gene_bed_maf_to_fasta_user_out.fasta" /> </test> diff -r f7459ad62be9 -r d669408018a1 tools/maf/interval_maf_to_merged_fasta.xml --- a/tools/maf/interval_maf_to_merged_fasta.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/maf/interval_maf_to_merged_fasta.xml Sun Sep 27 23:11:43 2009 -0400 @@ -49,10 +49,10 @@ </param> </when> </conditional> - <param name="overwrite_with_gaps" type="select" label="Split into Gapless MAF blocks" help="When set to Yes, blocks are divided around gaps appearing in any species. This will prevent gaps occuring in the interior of the sequence for an aligning species from overwriting a nucleotide found for the same position in a lower-scoring block."> + <param name="overwrite_with_gaps" type="select" label="Split into Gapless MAF blocks" help="When set to Yes, blocks are divided around gaps appearing in any species. This will prevent gaps occurring in the interior of the sequence for an aligning species from overwriting a nucleotide found for the same position in a lower-scoring block."> <option value="True" selected="true">No</option> <option value="False">Yes</option> - </param> + </param> </page> </inputs> <outputs> @@ -63,7 +63,7 @@ <param name="input1" value="13.bed" dbkey="hg18" ftype="bed"/> <param name="maf_source" value="cached"/> <param name="maf_identifier" value="17_WAY_MULTIZ_hg18"/> - <param name="species" value="hg18,mm8"/> + <param name="species" value="hg18,mm8"/> <param name="overwrite_with_gaps" value="True"/> <output name="out_file1" file="interval_maf_to_merged_fasta_out3.fasta" /> </test> @@ -71,7 +71,7 @@ <param name="input1" value="1.bed" dbkey="hg17" ftype="bed"/> <param name="maf_source" value="cached"/> <param name="maf_identifier" value="8_WAY_MULTIZ_hg17"/> - <param name="species" value="canFam1,hg17,mm5,panTro1,rn3"/> + <param name="species" value="canFam1,hg17,mm5,panTro1,rn3"/> <param name="overwrite_with_gaps" value="True"/> <output name="out_file1" file="interval_maf_to_merged_fasta_out.dat" /> </test> @@ -79,7 +79,7 @@ <param name="input1" value="1.bed" dbkey="hg17" ftype="bed"/> <param name="maf_source" value="user"/> <param name="maf_file" value="5.maf"/> - <param name="species" value="canFam1,hg17,mm5,panTro1,rn3"/> + <param name="species" value="canFam1,hg17,mm5,panTro1,rn3"/> <param name="overwrite_with_gaps" value="True"/> <output name="out_file1" file="interval_maf_to_merged_fasta_user_out.dat" /> </test> diff -r f7459ad62be9 -r d669408018a1 tools/maf/maf_to_bed.xml --- a/tools/maf/maf_to_bed.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/maf/maf_to_bed.xml Sun Sep 27 23:11:43 2009 -0400 @@ -36,12 +36,12 @@ * **Step 2 of 2**. Choose species from the alignment to be included in the output and specify how to deal with alignment blocks that lack one or more species: * **Choose species** - the tool reads the alignment provided during Step 1 and generates a list of species contained within that alignment. Using checkboxes you can specify taxa to be included in the output (only reference genome, shown in **bold**, is selected by default). If you select more than one species, then more than one history item will be created. - * **Choose to include/exclude blocks with missing species** - if an alignment block does not contain any one of the species you selected within **Choose species** menu and this option is set to **exclude blocks with missing species**, then coordiantes of such a block **will not** be included in the output (see **Example 2** below). + * **Choose to include/exclude blocks with missing species** - if an alignment block does not contain any one of the species you selected within **Choose species** menu and this option is set to **exclude blocks with missing species**, then coordinates of such a block **will not** be included in the output (see **Example 2** below). ----- -**Example 1**: **Include only refernce genome** (hg18 in this case) and **include blocks with missing species**: +**Example 1**: **Include only reference genome** (hg18 in this case) and **include blocks with missing species**: For the following alignment:: diff -r f7459ad62be9 -r d669408018a1 tools/maf/maf_to_fasta.xml --- a/tools/maf/maf_to_fasta.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/maf/maf_to_fasta.xml Sun Sep 27 23:11:43 2009 -0400 @@ -71,7 +71,7 @@ Multiple Block output has additional options: * **Choose species** - the tool reads the alignment provided during Step 1 and generates a list of species contained within that alignment. Using checkboxes you can specify taxa to be included in the output (all species are selected by default). - * **Choose to include/exclude blocks with missing species** - if an alignment block does not contain any one of the species you selected within **Choose species** menu and this option is set to **exclude blocks with missing species**, then such a block **will not** be included in the output (see **Example 2** below). For example, if you want to extact human, mouse, and rat from a series of alignments and one of the blocks does not contain mouse sequence, then this block will not be converted to FASTA and will not be returned. + * **Choose to include/exclude blocks with missing species** - if an alignment block does not contain any one of the species you selected within **Choose species** menu and this option is set to **exclude blocks with missing species**, then such a block **will not** be included in the output (see **Example 2** below). For example, if you want to extract human, mouse, and rat from a series of alignments and one of the blocks does not contain mouse sequence, then this block will not be converted to FASTA and will not be returned. ----- diff -r f7459ad62be9 -r d669408018a1 tools/maf/maf_to_interval.xml --- a/tools/maf/maf_to_interval.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/maf/maf_to_interval.xml Sun Sep 27 23:11:43 2009 -0400 @@ -1,5 +1,5 @@ <tool id="MAF_To_Interval1" name="MAF to Interval" force_history_refresh="True"> - <description>Converts a MAF formated file to the Interval format</description> + <description>Converts a MAF formatted file to the Interval format</description> <command interpreter="python">maf_to_interval.py $input1 $out_file1 $out_file1.id $__new_file_path__ $input1.dbkey $species $input1.metadata.species $complete_blocks $remove_gaps</command> <inputs> <param format="maf" name="input1" type="data" label="MAF file to convert"/> diff -r f7459ad62be9 -r d669408018a1 tools/metag_tools/blat_wrapper.xml --- a/tools/metag_tools/blat_wrapper.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/metag_tools/blat_wrapper.xml Sun Sep 27 23:11:43 2009 -0400 @@ -45,17 +45,17 @@ .. class:: warningmark - Use a smaller word size (*Minimal Size of Exact Match*) will increase the computational time. +Using a smaller word size (*Minimal Size of Exact Match*) will increase the computational time. .. class:: warningmark -Use a larger mismatch number (*Number of Mismatch in the Word*) will increase the computational time. +Using a larger mismatch number (*Number of Mismatch in the Word*) will increase the computational time. ----- **What it does** -This tool currently uses alignment program **BLAT**. Your short reads file is searched against a genome build or another uploaded file. +This tool currently uses the **BLAT** alignment program. Your short reads file is searched against a genome build or another uploaded file. ----- @@ -66,13 +66,13 @@ >seq1 TGGTAATGGTGGTTTTTTTTTTTTTTTTTTATTTTT -- Use default settings: +- Use the default settings: - alignment identity must be higher than or equal to 90%. - minimal size of exact match to trigger an alignment is 11. - - allow 0 mismatch in the above exact match size. + - allow 0 mismatches in the above exact match size. - Search against ce2 (C. elegans March 2004), partial result:: diff -r f7459ad62be9 -r d669408018a1 tools/metag_tools/convert_SOLiD_color2nuc.xml --- a/tools/metag_tools/convert_SOLiD_color2nuc.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/metag_tools/convert_SOLiD_color2nuc.xml Sun Sep 27 23:11:43 2009 -0400 @@ -25,13 +25,13 @@ .. class:: warningmark - The tool was designed for color space files generated from ABI SOLiD sequencer. The file format must be fasta-like: the title starts with a ">" sign, and each color space sequence starts with a leading nucleotide. +The tool was designed for color space files generated from an ABI SOLiD sequencer. The file format must be fasta-like: the title starts with a ">" character, and each color space sequence starts with a leading nucleotide. ----- **What it does** - This tool convert a color space sequence to nucleotides. The leading character must be one of the nucleotides: A, C, G, T. +This tool converts a color space sequence to nucleotides. The leading character must be a nucleotide: A, C, G, or T. ----- diff -r f7459ad62be9 -r d669408018a1 tools/metag_tools/mapping_to_ucsc.xml --- a/tools/metag_tools/mapping_to_ucsc.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/metag_tools/mapping_to_ucsc.xml Sun Sep 27 23:11:43 2009 -0400 @@ -145,7 +145,7 @@ **What it does** -This tool formats mapping data generated by short read mappers, as a custom track that can be displayed at UCSC genome browser. +This tool turns mapping data generated by short read mappers into a format that can be displayed in the UCSC genome browser as a custom track. ----- diff -r f7459ad62be9 -r d669408018a1 tools/metag_tools/megablast_xml_parser.xml --- a/tools/metag_tools/megablast_xml_parser.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/metag_tools/megablast_xml_parser.xml Sun Sep 27 23:11:43 2009 -0400 @@ -26,13 +26,13 @@ **What it does** -This tool will process XML output of any NCBI blast tool (if you run your own blast jobs, the XML output can be generated with **-m 7** option). +This tool processes the XML output of any NCBI blast tool (if you run your own blast jobs, the XML output can be generated with **-m 7** option). ----- **Output fields** -This tools returns tab-delimted output with the following fields:: +This tools returns tab-delimited output with the following fields:: Description Example ----------------------------------------- ----------------- diff -r f7459ad62be9 -r d669408018a1 tools/metag_tools/short_reads_figure_high_quality_length.xml --- a/tools/metag_tools/short_reads_figure_high_quality_length.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/metag_tools/short_reads_figure_high_quality_length.xml Sun Sep 27 23:11:43 2009 -0400 @@ -32,7 +32,7 @@ .. class:: warningmark - To use this tool your dataset needs to be in *Quality Score* format. Click pencil icon next to your dataset to set datatype to *Quality Score* (see below for examples of quality scores). +To use this tool, your dataset needs to be in the *Quality Score* format. Click the pencil icon next to your dataset to set the datatype to *Quality Score* (see below for examples). ----- @@ -62,7 +62,7 @@ >seq1 23 33 34 25 28 28 28 32 23 34 27 4 28 28 31 21 28 -- If the threshold was set to 20: +- If the threshold is set to 20: - a low quality score 4 in the middle separated two segments of lengths 11 and 5. diff -r f7459ad62be9 -r d669408018a1 tools/metag_tools/short_reads_figure_score.xml --- a/tools/metag_tools/short_reads_figure_score.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/metag_tools/short_reads_figure_score.xml Sun Sep 27 23:11:43 2009 -0400 @@ -29,7 +29,7 @@ .. class:: warningmark - To use this tool your dataset needs to be in *Quality Score* format. Click pencil icon next to your dataset to set datatype to *Quality Score* (see below for examples of quality scores). +To use this tool, your dataset needs to be in the *Quality Score* format. Click the pencil icon next to your dataset to set the datatype to *Quality Score* (see below for examples). ----- @@ -58,7 +58,7 @@ .. image:: ../static/images/short_reads_boxplot.png -where the **X-axis** is coordiante along the read and the **Y-axis** is quality score adjusted to comply with the Phred score metric. Units on the X-axis depend on whether your data comes from Roche (454) or Illumina (Solexa) and ABI SOLiD machines: +where the **X-axis** is coordinate along the read and the **Y-axis** is quality score adjusted to comply with the Phred score metric. Units on the X-axis depend on whether your data comes from Roche (454) or Illumina (Solexa) and ABI SOLiD machines: - For Roche (454) X-axis (shown above) indicates **relative** position (in %) within reads as this technology produces reads of different lengths; - For Illumina (Solexa) and ABI SOLiD X-axis shows **absolute** position in nucleotides within reads. diff -r f7459ad62be9 -r d669408018a1 tools/metag_tools/short_reads_trim_seq.xml --- a/tools/metag_tools/short_reads_trim_seq.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/metag_tools/short_reads_trim_seq.xml Sun Sep 27 23:11:43 2009 -0400 @@ -57,7 +57,7 @@ .. class:: warningmark - To use this tool your quality score dataset needs to be in *Quality Score* format. Click pencil icon next to your dataset to set datatype to *Quality Score*. +To use this tool, your dataset needs to be in the *Quality Score* format. Click the pencil icon next to your dataset to set the datatype to *Quality Score* (see below for examples). ----- diff -r f7459ad62be9 -r d669408018a1 tools/metag_tools/shrimp_color_wrapper.xml --- a/tools/metag_tools/shrimp_color_wrapper.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/metag_tools/shrimp_color_wrapper.xml Sun Sep 27 23:11:43 2009 -0400 @@ -55,7 +55,7 @@ .. class:: warningmark -To use this tool your dataset needs to be in *csfasta* (as ABI SOLiD color-space sequences) format. Click pencil icon next to your dataset to set datatype to *csfasta*. +To use this tool your dataset needs to be in the *csfasta* (as ABI SOLiD color-space sequences) format. Click pencil icon next to your dataset to set the datatype to *csfasta*. ----- @@ -166,8 +166,8 @@ -h S-W Full Hit Threshold (default: 68.00%) In letter-space, this parameter determines the threshold score for both vectored and full Smith-Waterman alignments. - Any values less than this quanitity will be thrown away. - *Note* This option differs slightly in meaning between letter-space and colour-space. + Any values less than this quantity will be thrown away. + *Note* This option differs slightly in meaning between letter-space and color-space. -v diff -r f7459ad62be9 -r d669408018a1 tools/metag_tools/shrimp_wrapper.xml --- a/tools/metag_tools/shrimp_wrapper.xml Sat Sep 26 18:05:36 2009 -0400 +++ b/tools/metag_tools/shrimp_wrapper.xml Sun Sep 27 23:11:43 2009 -0400 @@ -219,7 +219,7 @@ running time. Higher values will have the opposite effect. -t Seed Hit Taboo Length (default: 4) The seed taboo length specifies how many target genome bases - or colours must exist prior to a previous seed match in order + or colors must exist prior to a previous seed match in order to count another seed match as a hit. -9 Seed Generation Taboo Length (default: 0) @@ -265,8 +265,8 @@ -h S-W Hit Threshold (default: 68.00%) In letter-space, this parameter determines the threshold score for both vectored and full Smith-Waterman alignments. - Any values less than this quanitity will be thrown away. - *Note* This option differs slightly in meaning between letter-space and colour-space. + Any values less than this quantity will be thrown away. + *Note* This option differs slightly in meaning between letter-space and color-space. -----

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[hg] galaxy 2790: Paging for grids.
by Nate Coraor 02 Oct '09

02 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/4733c3b69226 changeset: 2790:4733c3b69226 user: jeremy goecks <jeremy.goecks at emory.edu> date: Mon Sep 28 10:29:23 2009 -0400 description: Paging for grids. 2 file(s) affected in this change: lib/galaxy/web/framework/helpers/grids.py templates/history/grid.mako diffs (128 lines): diff -r d669408018a1 -r 4733c3b69226 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Sun Sep 27 23:11:43 2009 -0400 +++ b/lib/galaxy/web/framework/helpers/grids.py Mon Sep 28 10:29:23 2009 -0400 @@ -4,7 +4,7 @@ from galaxy.web import url_for from galaxy.util.json import from_json_string, to_json_string -import sys, logging +import sys, logging, math log = logging.getLogger( __name__ ) @@ -23,6 +23,10 @@ default_filter = None default_sort_key = None preserve_state = False + + use_paging = False + num_rows_per_page = 5 + # Set preference names. cur_filter_pref_name = ".filter" cur_sort_key_pref_name = ".sort_key" @@ -90,7 +94,7 @@ column_filter = unicode(column_filter) extra_url_args[ "f-" + column.key ] = column_filter.encode("utf-8") - # Process sort arguments + # Process sort arguments. sort_key = sort_order = None if 'sort' in kwargs: sort_key = kwargs['sort'] @@ -110,7 +114,26 @@ # There might be a current row current_item = self.get_current_item( trans ) - # Save current filter and sort key. + # Process page number. + if self.use_paging: + if 'page' in kwargs: + page_num = int( kwargs['page'] ) + else: + page_num = 1 + + # Before modifying query, get the total number of rows that query returns so that the total number of pages can + # be computed. + total_num_rows = query.count() + query = query.limit( self.num_rows_per_page ).offset( ( page_num-1 ) * self.num_rows_per_page ) + + num_pages = int ( math.ceil( float( total_num_rows ) / self.num_rows_per_page ) ) + else: + # Defaults. + page_num = 1 + num_pages = 1 + + + # Preserve grid state: save current filter and sort key. if self.preserve_state: pref_name = unicode( self.__class__.__name__ + self.cur_filter_pref_name ) if not saved_filter_pref: @@ -146,9 +169,13 @@ else: new_kwargs[ 'id' ] = trans.security.encode_id( id ) return url_for( **new_kwargs ) + + return trans.fill_template( self.template, grid=self, query=query, + cur_page_num = page_num, + num_pages = num_pages, cur_filter_dict=cur_filter_dict, sort_key=sort_key, encoded_sort_key=encoded_sort_key, diff -r d669408018a1 -r 4733c3b69226 templates/history/grid.mako --- a/templates/history/grid.mako Sun Sep 27 23:11:43 2009 -0400 +++ b/templates/history/grid.mako Mon Sep 28 10:29:23 2009 -0400 @@ -299,20 +299,36 @@ </tr> %endfor </tbody> - %if grid.operations: - <tfoot> - <tr> - <td></td> - <td colspan="100"> - For <span class="grid-selected-count"></span> selected histories: - %for operation in grid.operations: - %if operation.allow_multiple: - <input type="submit" name="operation" value="${operation.label}" class="action-button"> - %endif - %endfor - </td> - </tr> - </tfoot> + <tfoot> + %if num_pages > 1: + <tr> + <td></td> + <td colspan="100" style="font-size: 90%; text-align: right"> + Page: + %for page_index in range(1, num_pages + 1): + %if page_index == cur_page_num: + <span style="font-style: italic">${page_index}</span> + %else: + <% args = { "page" : page_index } %> + <span><a href="${url( args )}">${page_index}</a></span> + %endif + %endfor + </td> + </tr> + %endif + %if grid.operations: + <tr> + <td></td> + <td colspan="100"> + For <span class="grid-selected-count"></span> selected histories: + %for operation in grid.operations: + %if operation.allow_multiple: + <input type="submit" name="operation" value="${operation.label}" class="action-button"> + %endif + %endfor + </td> + </tr> + </tfoot> %endif </table> </form>

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[hg] galaxy 2791: fix history grids
by Nate Coraor 02 Oct '09

02 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/40c3c7798b64 changeset: 2791:40c3c7798b64 user: Kanwei Li <kanwei(a)gmail.com> date: Mon Sep 28 12:39:53 2009 -0400 description: fix history grids 2 file(s) affected in this change: templates/grid.mako templates/history/grid.mako diffs (100 lines): diff -r 4733c3b69226 -r 40c3c7798b64 templates/grid.mako --- a/templates/grid.mako Mon Sep 28 10:29:23 2009 -0400 +++ b/templates/grid.mako Mon Sep 28 12:39:53 2009 -0400 @@ -214,19 +214,19 @@ %endfor </tbody> %if grid.has_multiple_item_operations: - <tfoot> - <tr> - <td></td> - <td colspan="100"> - For <span class="grid-selected-count"></span> selected items: - %for operation in grid.operations: - %if operation.allow_multiple: - <input type="submit" name="operation" value="${operation.label}" class="action-button"> - %endif - %endfor - </td> - </tr> - </tfoot> + <tfoot> + <tr> + <td></td> + <td colspan="100"> + For <span class="grid-selected-count"></span> selected items: + %for operation in grid.operations: + %if operation.allow_multiple: + <input type="submit" name="operation" value="${operation.label}" class="action-button"> + %endif + %endfor + </td> + </tr> + </tfoot> %endif </table> </form> diff -r 4733c3b69226 -r 40c3c7798b64 templates/history/grid.mako --- a/templates/history/grid.mako Mon Sep 28 10:29:23 2009 -0400 +++ b/templates/history/grid.mako Mon Sep 28 12:39:53 2009 -0400 @@ -301,34 +301,34 @@ </tbody> <tfoot> %if num_pages > 1: - <tr> - <td></td> - <td colspan="100" style="font-size: 90%; text-align: right"> - Page: - %for page_index in range(1, num_pages + 1): - %if page_index == cur_page_num: - <span style="font-style: italic">${page_index}</span> - %else: - <% args = { "page" : page_index } %> - <span><a href="${url( args )}">${page_index}</a></span> - %endif - %endfor - </td> - </tr> + <tr> + <td></td> + <td colspan="100" style="font-size: 90%; text-align: right"> + Page: + %for page_index in range(1, num_pages + 1): + %if page_index == cur_page_num: + <span style="font-style: italic">${page_index}</span> + %else: + <% args = { "page" : page_index } %> + <span><a href="${url( args )}">${page_index}</a></span> + %endif + %endfor + </td> + </tr> %endif %if grid.operations: - <tr> - <td></td> - <td colspan="100"> - For <span class="grid-selected-count"></span> selected histories: - %for operation in grid.operations: - %if operation.allow_multiple: - <input type="submit" name="operation" value="${operation.label}" class="action-button"> - %endif - %endfor - </td> - </tr> + <tr> + <td></td> + <td colspan="100"> + For <span class="grid-selected-count"></span> selected histories: + %for operation in grid.operations: + %if operation.allow_multiple: + <input type="submit" name="operation" value="${operation.label}" class="action-button"> + %endif + %endfor + </td> + </tr> + %endif </tfoot> - %endif </table> </form>

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galaxy-dev October 2009