- galaxy-commits - lists.galaxyproject.org

[hg] galaxy 3754: Replace large selects w/o refresh_on_change wi...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/f550290ed5ad changeset: 3754:f550290ed5ad user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Fri May 07 09:16:51 2010 -0400 description: Replace large selects w/o refresh_on_change with search+select. diffstat: static/scripts/galaxy.base.js | 12 ++++++++---- 1 files changed, 8 insertions(+), 4 deletions(-) diffs (24 lines): diff -r e42d0ae7b789 -r f550290ed5ad static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js Fri May 07 08:52:43 2010 -0400 +++ b/static/scripts/galaxy.base.js Fri May 07 09:16:51 2010 -0400 @@ -145,12 +145,16 @@ } // Replace select box with a text input box + autocomplete. -// TODO: make work with dynamic tool inputs and then can replace all big selects. +// TODO: make work with selects where refresh_on_change=True and refresh_on_change_values="..." function replace_big_select_inputs(min_length) { - $('select[name=dbkey]').each( function() { + // Set default for min_length. + if (min_length === undefined) + min_length = 20; + + $('select[refresh_on_change!="true"]').each( function() { var select_elt = $(this); - // Skip if # of options < threshold - if (min_length !== undefined && select_elt.find('option').length < min_length) + // Skip if # of options < min length. + if (select_elt.find('option').length < min_length) return; // Replace select with text + autocomplete.

1 0

[hg] galaxy 3753: Fix grid filtering bug.
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/e42d0ae7b789 changeset: 3753:e42d0ae7b789 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Fri May 07 08:52:43 2010 -0400 description: Fix grid filtering bug. diffstat: templates/grid_base.mako | 9 ++++++--- 1 files changed, 6 insertions(+), 3 deletions(-) diffs (19 lines): diff -r 8fdcfecfe856 -r e42d0ae7b789 templates/grid_base.mako --- a/templates/grid_base.mako Thu May 06 19:39:27 2010 -0400 +++ b/templates/grid_base.mako Fri May 07 08:52:43 2010 -0400 @@ -248,9 +248,12 @@ var url_args = ${h.to_json_string( cur_filter_dict )}; // Place "f-" in front of all filter arguments. - $.map(url_args, function(arg) { - return "f-" + arg; - }); + for (arg in url_args) + { + value = url_args[arg]; + delete url_args[arg]; + url_args["f-" + arg] = value; + } // Add sort argument to URL args. url_args['sort'] = "${encoded_sort_key}";

1 0

[hg] galaxy 3752: Add the modENCODEfly and modENCODEworm data so...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/8fdcfecfe856 changeset: 3752:8fdcfecfe856 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Thu May 06 19:39:27 2010 -0400 description: Add the modENCODEfly and modENCODEworm data source tools. diffstat: tools/data_source/fly_modencode.xml | 27 +++++++++++++++++++++++++++ tools/data_source/worm_modencode.xml | 27 +++++++++++++++++++++++++++ 2 files changed, 54 insertions(+), 0 deletions(-) diffs (62 lines): diff -r d3268bb6e48a -r 8fdcfecfe856 tools/data_source/fly_modencode.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/data_source/fly_modencode.xml Thu May 06 19:39:27 2010 -0400 @@ -0,0 +1,27 @@ +<?xml version="1.0"?> +<tool name="modENCODE fly" id="modENCODEfly" tool_type="data_source"> + <description>server</description> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> + <inputs action="http://modencode.oicr.on.ca/fgb2/gbrowse/fly" check_values="false" target="_top"> + <display>go to modENCODE fly server $GALAXY_URL</display> + <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=modENCODEfly" /> + </inputs> + <request_param_translation> + <request_param galaxy_name="URL" remote_name="URL" missing=""> + <append_param separator="&" first_separator="?" join="="> + <value name="d" missing="" /> + <value name="dbkey" missing="" /> + <value name="q" missing="" /> + <value name="s" missing="" /> + <value name="t" missing="" /> + </append_param> + </request_param> + <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" /> + <request_param galaxy_name="data_type" remote_name="data_type" missing="txt" /> + </request_param_translation> + <uihints minwidth="800"/> + <outputs> + <data name="output" format="txt" /> + </outputs> + <options sanitize="False" refresh="True"/> +</tool> diff -r d3268bb6e48a -r 8fdcfecfe856 tools/data_source/worm_modencode.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/data_source/worm_modencode.xml Thu May 06 19:39:27 2010 -0400 @@ -0,0 +1,27 @@ +<?xml version="1.0"?> +<tool name="modENCODE worm" id="modENCODEworm" tool_type="data_source"> + <description>server</description> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> + <inputs action="http://modencode.oicr.on.ca/fgb2/gbrowse/worm" check_values="false" target="_top"> + <display>go to modENCODE worm server $GALAXY_URL</display> + <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=modENCODEworm" /> + </inputs> + <request_param_translation> + <request_param galaxy_name="URL" remote_name="URL" missing=""> + <append_param separator="&" first_separator="?" join="="> + <value name="d" missing="" /> + <value name="dbkey" missing="" /> + <value name="q" missing="" /> + <value name="s" missing="" /> + <value name="t" missing="" /> + </append_param> + </request_param> + <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" /> + <request_param galaxy_name="data_type" remote_name="data_type" missing="txt" /> + </request_param_translation> + <uihints minwidth="800"/> + <outputs> + <data name="output" format="txt" /> + </outputs> + <options sanitize="False" refresh="True"/> +</tool>

1 0

[hg] galaxy 3751: Fix bug that was preventing annotation of work...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/d3268bb6e48a changeset: 3751:d3268bb6e48a user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Thu May 06 17:52:49 2010 -0400 description: Fix bug that was preventing annotation of workflow input datasets. diffstat: templates/workflow/editor_generic_form.mako | 76 ++++++++++++++-------------- 1 files changed, 38 insertions(+), 38 deletions(-) diffs (84 lines): diff -r 370777a0693f -r d3268bb6e48a templates/workflow/editor_generic_form.mako --- a/templates/workflow/editor_generic_form.mako Thu May 06 12:30:54 2010 -0400 +++ b/templates/workflow/editor_generic_form.mako Thu May 06 17:52:49 2010 -0400 @@ -1,42 +1,42 @@ -<div class="toolForm"> - <div class="toolFormTitle">${form.title}</div> - <div class="toolFormBody"> - <form name="${form.name}" action="${h.url_for( action='editor_form_post' )}" method="post"> - <input type="hidden" name="type" value="${module.type}" /> - %if form.inputs: - %for input in form.inputs: - <% - cls = "form-row" - if input.error: - cls += " form-row-error" - %> - <div class="${cls}"> - <label> - ${input.label}: - </label> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="${input.type}" name="${input.name | h}" value="${input.value | h}" size="30"> - </div> - %if input.error: - <div style="float: left; color: red; font-weight: bold; padding-top: 1px; padding-bottom: 3px;"> - <div style="width: 300px;"><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${input.error}</span></div> - </div> - %endif +<form name="${form.name}" action="${h.url_for( action='editor_form_post' )}" method="post"> + <div class="toolForm"> + <div class="toolFormTitle">${form.title}</div> + <div class="toolFormBody"> + <input type="hidden" name="type" value="${module.type}" /> + %if form.inputs: + %for input in form.inputs: + <% + cls = "form-row" + if input.error: + cls += " form-row-error" + %> + <div class="${cls}"> + <label> + ${input.label}: + </label> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="${input.type}" name="${input.name | h}" value="${input.value | h}" size="30"> + </div> + %if input.error: + <div style="float: left; color: red; font-weight: bold; padding-top: 1px; padding-bottom: 3px;"> + <div style="width: 300px;"><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${input.error}</span></div> + </div> + %endif - %if input.help: - <div class="toolParamHelp" style="clear: both;"> - ${input.help} - </div> - %endif + %if input.help: + <div class="toolParamHelp" style="clear: both;"> + ${input.help} + </div> + %endif - <div style="clear: both"></div> + <div style="clear: both"></div> - </div> - %endfor - %else: - <div class="form-row"><i>No options</i></div> - %endif - </table> - </form> + </div> + %endfor + %else: + <div class="form-row"><i>No options</i></div> + %endif + </table> + </div> </div> -</div> +</form>

1 0

[hg] galaxy 3750: trackster:
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/370777a0693f changeset: 3750:370777a0693f user: Kanwei Li <kanwei(a)gmail.com> date: Thu May 06 12:30:54 2010 -0400 description: trackster: - Custom dbkeys now create new HDA and copies info in - Fix track reordering for all browsers - Fix track deletion - Fix BAM display diffstat: lib/galaxy/visualization/tracks/data/bam.py | 6 ++-- lib/galaxy/web/controllers/tracks.py | 35 ++++++++++++++++++---------- lib/galaxy/web/controllers/user.py | 19 +++++++++++++-- static/scripts/packed/trackster.js | 2 +- static/scripts/trackster.js | 28 ++++++++++++++--------- templates/tracks/browser.mako | 4 +-- templates/user/dbkeys.mako | 25 +++++++++++--------- tool_conf.xml.main | 1 + 8 files changed, 75 insertions(+), 45 deletions(-) diffs (294 lines): diff -r e7d91d58f4ad -r 370777a0693f lib/galaxy/visualization/tracks/data/bam.py --- a/lib/galaxy/visualization/tracks/data/bam.py Thu May 06 12:11:47 2010 -0400 +++ b/lib/galaxy/visualization/tracks/data/bam.py Thu May 06 12:30:54 2010 -0400 @@ -10,7 +10,7 @@ import logging log = logging.getLogger(__name__) -MAX_VALS = 50 # only display first MAX_VALS datapoints +MAX_VALS = 5000 # only display first MAX_VALS datapoints class BamDataProvider( object ): """ @@ -36,7 +36,7 @@ if chrom.startswith( 'chr' ): try: data = bamfile.fetch( start=start, end=end, reference=chrom[3:] ) - except: + except ValueError: return None else: return None @@ -74,4 +74,4 @@ results.append( [ qname, start, end, read['seq'], r1, r2 ] ) bamfile.close() - return results \ No newline at end of file + return { 'data': results, 'message': message } diff -r e7d91d58f4ad -r 370777a0693f lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py Thu May 06 12:11:47 2010 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Thu May 06 12:30:54 2010 -0400 @@ -99,7 +99,7 @@ user = trans.get_user() if 'dbkeys' in user.preferences: user_keys = from_json_string( user.preferences['dbkeys'] ) - + dbkeys = [ (k, v) for k, v in trans.db_builds if k in self.len_files or k in user_keys ] return trans.fill_template( "tracks/new_browser.mako", dbkeys=dbkeys ) @@ -197,21 +197,24 @@ """ Helper method that returns chrom lengths for a given user and dbkey. """ + len_file = None + len_ds = None # If there is any dataset in the history of extension `len`, this will use it if 'dbkeys' in user.preferences: user_keys = from_json_string( user.preferences['dbkeys'] ) if dbkey in user_keys: - return user_keys[dbkey]['chroms'] + len_file = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( user_keys[dbkey]['len'] ).file_name - db_manifest = trans.db_dataset_for( dbkey ) - if not db_manifest: - db_manifest = os.path.join( trans.app.config.tool_data_path, 'shared','ucsc','chrom', "%s.len" % dbkey ) - else: - db_manifest = db_manifest.file_name + if not len_file: + len_ds = trans.db_dataset_for( dbkey ) + if not len_ds: + len_file = os.path.join( trans.app.config.tool_data_path, 'shared','ucsc','chrom', "%s.len" % dbkey ) + else: + len_file = len_ds.file_name manifest = {} - if not os.path.exists( db_manifest ): + if not os.path.exists( len_file ): return None - for line in open( db_manifest ): + for line in open( len_file ): if line.startswith("#"): continue line = line.rstrip("\r\n") fields = line.split("\t") @@ -240,7 +243,9 @@ # Need to check states again for the converted version if converted_dataset and converted_dataset.state == model.Dataset.states.ERROR: - return messages.ERROR + job_id = trans.sa_session.query( trans.app.model.JobToOutputDatasetAssociation ).filter_by( dataset_id=converted_dataset.id ).first().job_id + job = trans.sa_session.query( trans.app.model.Job ).get( job_id ) + return { 'kind': messages.ERROR, 'message': job.stderr } if not converted_dataset or converted_dataset.state != model.Dataset.states.OK: return messages.PENDING @@ -256,13 +261,17 @@ extra_info = "no_detail" else: frequencies, max_v, avg_v, delta = summary - return { "dataset_type": data_sources['index'], "data": frequencies, "max": max_v, "avg": avg_v, "delta": delta } + return { 'dataset_type': data_sources['index'], 'data': frequencies, 'max': max_v, 'avg': avg_v, 'delta': delta } dataset_type = data_sources['data'] data_provider = dataset_type_to_data_provider[ dataset_type ]( dataset.get_converted_dataset(trans, dataset_type), dataset ) - + data = data_provider.get_data( chrom, low, high, **kwargs ) - return { "dataset_type": dataset_type, "extra_info": extra_info, "data": data } + message = None + if isinstance(data, dict) and 'message' in data: + message = data['message'] + data = data['data'] + return { 'dataset_type': dataset_type, 'extra_info': extra_info, 'data': data, 'message': message } @web.expose def list_tracks( self, trans, hid ): diff -r e7d91d58f4ad -r 370777a0693f lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py Thu May 06 12:11:47 2010 -0400 +++ b/lib/galaxy/web/controllers/user.py Thu May 06 12:30:54 2010 -0400 @@ -902,7 +902,18 @@ if not name or not key or not len_text: message = "You must specify values for all the fields." else: - chrom_dict = {} + # Create new len file + new_len = trans.app.model.HistoryDatasetAssociation( extension="len", create_dataset=True, sa_session=trans.sa_session ) + trans.sa_session.add( new_len ) + new_len.name = name + new_len.visible = False + new_len.history_id = trans.get_history().id + new_len.state = trans.app.model.Job.states.OK + new_len.info = "custom build .len file" + trans.sa_session.flush() + + counter = 0 + f = open(new_len.file_name, "w") for line in len_text.split("\n"): lst = line.strip().split() if not lst or len(lst) < 2: @@ -914,8 +925,10 @@ except ValueError: lines_skipped += 1 continue - chrom_dict[chrom] = length - dbkeys[key] = { "name": name, "chroms": chrom_dict } + counter += 1 + f.write("%s\t%s\n" % (chrom, length)) + f.close() + dbkeys[key] = { "name": name, "len": new_len.id, "count": counter } user.preferences['dbkeys'] = to_json_string(dbkeys) trans.sa_session.flush() diff -r e7d91d58f4ad -r 370777a0693f static/scripts/packed/trackster.js --- a/static/scripts/packed/trackster.js Thu May 06 12:11:47 2010 -0400 +++ b/static/scripts/packed/trackster.js Thu May 06 12:30:54 2010 -0400 @@ -1,1 +1,1 @@ -var DEBUG=false;var DENSITY=200,FEATURE_LEVELS=10,DATA_ERROR="There was an error in indexing this dataset.",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=5,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="/static/images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="/static/images/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src="/static/images/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(! right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src="/static/images/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var Drawer=function(){};$.extend(Drawer.prototype,{intensity:function(b,a,c){},});drawer=new Drawer();var View=function(b,d,c,a){this.vis_id=c;this.dbkey=a;this.title=d;this.chrom=b;this.tracks=[];this.label_tracks=[];this.m! ax_low=0;this.max_high=0;this.center=(this.max_high-this.max_low)/2;th is.zoom_factor=3;this.zoom_level=0;this.track_id_counter=0};$.extend(View.prototype,{add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.track_id_counter+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[a]},update_options:function(){var b=$("ul#sortable-ul").sortable("toArray");var d=[];var c=$("#viewport > div").sort(function(g,f){return b.indexOf($(g).attr("id"))>b.indexOf($(f).attr("id"))});$("#viewport > div").remove();$("#viewport").html(c);for(var e in view.tracks){var a=view.tracks[e];if(a.update_options){a.update_options(e)}}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.center=this.center=(this.max_high-this.max_low)/2;this.zoom_level=0;$(".yaxislabel").remove()},redraw:function(f){this.span=this.max_high-this.max! _low;var d=this.span/Math.pow(this.zoom_factor,this.zoom_level),b=this.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));if(!f){for(var c=0,a=this.tracks.length;c<a;c++){if(this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,a=this.label_tracks.length;c<a;c++){this.label_tracks[c].draw()}}},zoom_in:function(a,b){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=! a/b.width()*(this.high-this.low)+this.low}this.zoom_level+=1;this.redr aw()},zoom_out:function(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.init_global()};$.extend(Track.prototype,{init_global:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div></div>").addClass("track").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.content_div.css("height","30px");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(d==="no converter"){a.container_div.addClass("error");a.cont! ent_div.text(DATA_NOCONVERTER)}else{if(d.data&&d.data.length===0||d.data===null){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var i=this.view.low,e=this.view.high,f=e-i,d=this.view.resolution;if(DEBUG){$("#debug").text(d+" "+this.view.zoom_res)}var k=$("<div style='position: relative;'></div>"),l=this.content_div.width()/f,h;this.content_div.children(":first").remove();this.content_div.append(k),this.max_height=0;var a=Math.floor(i/d/DENSITY);while((a*DENSITY*d)<e){var j=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var c=this.tile_cache.get(j);if(c! ){var g=a*DENSITY*d;var b=(g-i)*l;if(this.left_offset){b-=this.left_of fset}c.css({left:b});k.append(c);this.max_height=Math.max(this.max_height,c.height());this.content_div.css("height",this.max_height+"px")}else{this.delayed_draw(this,j,i,e,a,d,k,l)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height+"px")}}},50)}});var LabelTrack=function(a){Track.call(this,null,a);this.track_type="LabelTrack";this.hidden=true;this.container_div.addClass("label-track")};$.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'>"+commatize(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,a,b){this.track_type="LineTrack";Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.height_px=100;this.container_div.addClass("line-track");this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={min_value:undefined,max_value:undefined,mode:"Line"};if(b.min_value!==undefined){this.prefs.min_value=b.min_value}if(b.max_value!==undefined){this.prefs.max_value=b.max_value}if(b.mode!==undefined){this.prefs.mode=b.mode}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.ma! x_value=data.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#t rack_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;$("#linetrack_"+b+"_minval").remove();$("#linetrack_"+b+"_maxval").remove();var e=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(a.prefs.min_value);var d=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(a.prefs.max_value);d.css({position:"relative",top:"25px"});d.prependTo(a.container_div);e.css({position:"relative",top:a.height_px+55+"px"});e.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o! ,q,c,e){if(this.vertical_range===undefined){return}var r=q*DENSITY*o,a=DENSITY*o,b=$("<canvas class='tile'></canvas>"),u=o+"_"+q;if(this.data_cache.get(u)===undefined){this.get_data(o,q);return}var t=this.data_cache.get(u);if(t===null){return}b.css({position:"absolute",top:0,left:(r-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,s=this.total_frequency,d=this.height_px;n.beginPath();if(t.length>1){var f=Math.ceil((t[1][0]-t[0][0])*e)}else{var f=10}for(var p=0;p<t.length;p++){var j=t[p][0]-r;var h=t[p][1];if(this.prefs.mode=="Intensity"){if(h===null){continue}j=j*e;if(h<=l){h=l}else{if(h>=g){h=g}}h=255-Math.floor((h-l)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(j,0,f,this.height_px)}else{if(h===null){k=false;continue}else{j=j*e;if(h<=l){h=l}else{if(h>=g){h=g}}h=Math.round(d-(h-l)/m*d);if(k){n.lineTo(j,h)}else{n.moveTo(j,h);k=! true}}}}n.stroke();c.append(b);return b},gen_options:function(n){var a =$("<div></div>").addClass("form-row");var h="track_"+n+"_minval",k="track_"+n+"_maxval",e="track_"+n+"_mode",l=$("<label></label>").attr("for",h).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),m=$("<input></input>").attr("id",h).val(b),g=$("<label></label>").attr("for",k).text("Max value:"),j=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",k).val(j),d=$("<label></label>").attr("for",e).text("Display mode:"),i=(this.prefs.mode===undefined?"Line":this.prefs.mode),c=$('<select id="'+e+'"><option value="Line" id="mode_Line">Line</option><option value="Intensity" id="mode_Intensity">Intensity</option></select>');c.children("#mode_"+i).attr("selected","selected");return a.append(l).append(m).append(g).append(f).append(d).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_mode option:selected").val();if(a!==this.prefs.min_value||c!! ==this.prefs.max_value||b!=this.prefs.mode){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.mode=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(c,a,b){this.track_type="FeatureTrack";Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.height_px=100;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.default_font="9px Monaco, Lucida Console, monospace";this.left_offset=200;this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.prefs={block_color:"black",label_color:"black",show_counts:false};if(b.block_color!==undefine! d){this.prefs.block_color=b.block_color}if(b.label_color!==undefined){ this.prefs.label_color=b.label_color}if(b.show_counts!==undefined){this.prefs.show_counts=b.show_counts}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.max_low+"_"+a.view.max_high;this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution},function(c){a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolution},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,g,c){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=1/a;this.s_e_by_tile[a]={}}var m=this.inc_slots[a].w_scale,v=[],h=0,b=$("<canvas></canvas>").get(0).getContext("2d"),n=this.view.max_low;var d,f,x=[];for(var s=0,t=g.length;s<t;s++){var e=g[s],l=e[0];if(this.inc_slots[! a][l]!==undefined){h=Math.max(h,this.inc_slots[a][l]);x.push(this.inc_slots[a][l])}else{v.push(s)}}for(var s=0,t=v.length;s<t;s++){var e=g[v[s]];l=e[0],feature_start=e[1],feature_end=e[2],feature_name=e[3];d=Math.floor((feature_start-n)*m);f=Math.ceil((feature_end-n)*m);if(!c){var p=b.measureText(feature_name).width;if(d-p<0){f+=p}else{d-=p}}var r=0;while(true){var o=true;if(this.s_e_by_tile[a][r]!==undefined){for(var q=0,w=this.s_e_by_tile[a][r].length;q<w;q++){var u=this.s_e_by_tile[a][r][q];if(f>u[0]&&d<u[1]){o=false;break}}}if(o){if(this.s_e_by_tile[a][r]===undefined){this.s_e_by_tile[a][r]=[]}this.s_e_by_tile[a][r].push([d,f]);this.inc_slots[a][l]=r;h=Math.max(h,r);break}r++}}return h},rect_or_text:function(n,o,g,f,m,b,d,k,e,i){n.textAlign="center";var j=Math.round(o/2);if(d!==undefined&&o>g){n.fillStyle="#555";n.fillRect(k,i+1,e,9);n.fillStyle="#eee";for(var h=0,l=d.length;h<l;h++){if(b+h>=f&&b+h<=m){var a=Math.floor(Math.max(0,(b+h-f)*o));n.fillText(d[h],a+this.left_! offset+j,i+9)}}}else{n.fillStyle="#555";n.fillRect(k,i+4,e,3)}},draw_t ile:function(W,h,m,ak){var D=h*DENSITY*W,ac=(h+1)*DENSITY*W,C=DENSITY*W;var aj,r;var ad=D+"_"+ac;var w=this.data_cache.get(ad);if(w===undefined){this.data_queue[[D,ac]]=true;this.get_data(D,ac);return}if(w.dataset_type==="summary_tree"){r=30}else{var U=(w.extra_info==="no_detail");var al=(U?this.vertical_nodetail_px:this.vertical_detail_px);r=this.incremental_slots(this.view.zoom_res,w.data,U)*al+15;m.parent().css("height",Math.max(this.height_px,r)+"px");aj=this.inc_slots[this.view.zoom_res]}var a=Math.ceil(C*ak),K=$("<canvas class='tile'></canvas>"),Y=this.prefs.label_color,f=this.prefs.block_color,O=this.left_offset;K.css({position:"absolute",top:0,left:(D-this.view.low)*ak-O});K.get(0).width=a+O;K.get(0).height=r;var z=K.get(0).getContext("2d"),ah=z.measureText("A").width;z.fillStyle=this.prefs.block_color;z.font=this.default_font;z.textAlign="right";if(w.dataset_type=="summary_tree"){var J,G=55,ab=255-G,g=ab*2/3,Q=w.data,B=w.max,l=w.avg;if(Q.length>2){var b=Math.ceil((Q! [1][0]-Q[0][0])*ak)}else{var b=50}for(var af=0,v=Q.length;af<v;af++){var S=Math.ceil((Q[af][0]-D)*ak);var R=Q[af][1];if(!R){continue}J=Math.floor(ab-(R/B)*ab);z.fillStyle="rgb("+J+","+J+","+J+")";z.fillRect(S+O,0,b,20);if(this.prefs.show_counts){if(J>g){z.fillStyle="black"}else{z.fillStyle="#ddd"}z.textAlign="center";z.fillText(Q[af][1],S+O+(b/2),12)}}m.append(K);return K}var ai=w.data;var ae=0;for(var af=0,v=ai.length;af<v;af++){var L=ai[af],I=L[0],ag=L[1],T=L[2],E=L[3];if(ag<=ac&&T>=D){var V=Math.floor(Math.max(0,(ag-D)*ak)),A=Math.ceil(Math.min(a,Math.max(0,(T-D)*ak))),P=aj[I]*al;if(w.dataset_type==="bai"){z.fillStyle="#555";if(L[4] instanceof Array){var s=Math.floor(Math.max(0,(L[4][0]-D)*ak)),H=Math.ceil(Math.min(a,Math.max(0,(L[4][1]-D)*ak))),q=Math.floor(Math.max(0,(L[5][0]-D)*ak)),o=Math.ceil(Math.min(a,Math.max(0,(L[5][1]-D)*ak)));if(L[4][1]>=D&&L[4][0]<=ac){this.rect_or_text(z,ak,ah,D,ac,L[4][0],L[4][2],s+O,H-s,P)}if(L[5][1]>=D&&L[5][0]<=ac){this.rect_or_text(z,ak! ,ah,D,ac,L[5][0],L[5][2],q+O,o-q,P)}if(q>H){z.fillStyle="#999";z.fillR ect(H+O,P+5,q-H,1)}}else{z.fillStyle="#555";this.rect_or_text(z,ak,ah,D,ac,ag,E,V+O,A-V,P)}if(!U&&ag>D){z.fillStyle=this.prefs.label_color;if(h===0&&V-z.measureText(E).width<0){z.textAlign="left";z.fillText(I,A+2+O,P+8)}else{z.textAlign="right";z.fillText(I,V-2+O,P+8)}z.fillStyle="#555"}}else{if(w.dataset_type==="interval_index"){if(U){z.fillRect(V+O,P+5,A-V,1)}else{var u=L[4],N=L[5],X=L[6],e=L[7];var t,Z,F=null,am=null;if(N&&X){F=Math.floor(Math.max(0,(N-D)*ak));am=Math.ceil(Math.min(a,Math.max(0,(X-D)*ak)))}if(E!==undefined&&ag>D){z.fillStyle=Y;if(h===0&&V-z.measureText(E).width<0){z.textAlign="left";z.fillText(E,A+2+O,P+8)}else{z.textAlign="right";z.fillText(E,V-2+O,P+8)}z.fillStyle=f}if(e){if(u){if(u=="+"){z.fillStyle=RIGHT_STRAND}else{if(u=="-"){z.fillStyle=LEFT_STRAND}}z.fillRect(V+O,P,A-V,10);z.fillStyle=f}for(var ad=0,d=e.length;ad<d;ad++){var n=e[ad],c=Math.floor(Math.max(0,(n[0]-D)*ak)),M=Math.ceil(Math.min(a,Math.max((n[1]-D)*ak)));if(c>M){continue}t=5;Z=3;z.fillR! ect(c+O,P+Z,M-c,t);if(F!==undefined&&!(c>am||M<F)){t=9;Z=1;var aa=Math.max(c,F),p=Math.min(M,am);z.fillRect(aa+O,P+Z,p-aa,t)}}}else{t=9;Z=1;z.fillRect(V+O,P+Z,A-V,t);if(L.strand){if(L.strand=="+"){z.fillStyle=RIGHT_STRAND_INV}else{if(L.strand=="-"){z.fillStyle=LEFT_STRAND_INV}}z.fillRect(V+O,P,A-V,10);z.fillStyle=prefs.block_color}}}}}ae++}}m.append(K);return K},gen_options:function(i){var a=$("<div></div>").addClass("form-row");var e="track_"+i+"_block_color",k=$("<label></label>").attr("for",e).text("Block color:"),l=$("<input></input>").attr("id",e).attr("name",e).val(this.prefs.block_color),j="track_"+i+"_label_color",g=$("<label></label>").attr("for",j).text("Text color:"),h=$("<input></input>").attr("id",j).attr("name",j).val(this.prefs.label_color),f="track_"+i+"_show_count",c=$("<label></label>").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$(! "<div></div>").append(b).append(c);return a.append(k).append(l).append (g).append(h).append(d)},update_options:function(d){var b=$("#track_"+d+"_block_color").val(),c=$("#track_"+d+"_label_color").val(),a=$("#track_"+d+"_show_count").attr("checked");if(b!==this.prefs.block_color||c!==this.prefs.label_color||a!=this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=c;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(c,a,b){FeatureTrack.call(this,c,a,b);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{}); \ No newline at end of file +var DEBUG=false;var DENSITY=200,FEATURE_LEVELS=10,DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=5,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="/static/images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="/static/images/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src="/static/images/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern! (right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src="/static/images/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var Drawer=function(){};$.extend(Drawer.prototype,{intensity:function(b,a,c){},});drawer=new Drawer();var View=function(b,d,c,a){this.vis_id=c;this.dbkey=a;this.title=d;this.chrom=b;this.tracks=[];this.label_tracks=[];this.! max_low=0;this.max_high=0;this.center=(this.max_high-this.max_low)/2;t his.zoom_factor=3;this.zoom_level=0;this.track_id_counter=0};$.extend(View.prototype,{add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.track_id_counter+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks.splice(this.tracks.indexOf(a))},update_options:function(){var b=$("ul#sortable-ul").sortable("toArray");for(var c in b){var e=b[c].split("_li")[0].split("track_")[1];$("#viewport").append($("#track_"+e))}for(var d in view.tracks){var a=view.tracks[d];if(a.update_options){a.update_options(d)}}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.center=this.center=(this.max_high-this.max_low)/2;this.zoom_level=0;$(".yaxislabel").remove()},redraw:function(f){this.span=this.max_high-this.max_low;var d=this.span/Math.pow(this.zoom_fa! ctor,this.zoom_level),b=this.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));if(!f){for(var c=0,a=this.tracks.length;c<a;c++){if(this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,a=this.label_tracks.length;c<a;c++){this.label_tracks[c].draw()}}},zoom_in:function(a,b){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/b.width()*(this.high-this.low)+this.low}! this.zoom_level+=1;this.redraw()},zoom_out:function(){if(this.max_high ===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.init_global()};$.extend(Track.prototype,{init_global:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div></div>").addClass("track").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.content_div.css("height","30px");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"||d.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(d.message){var f=a.view.tracks.indexOf(a);var e=$("<a href='javascript:void(0);'></a>").a! ttr("id",f+"_error");e.text("Click to view error");$("#"+f+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+d.message+"</pre>",{Close:hide_modal})});a.content_div.append(e)}}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.data!==undefined&&(d.data===null||d.data.length===0)){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var i=this.view.low,e=this.view.high,f=e-i,d=this.view.resolution;if(DEBUG){$("#debug").text(d+" "+this.view.zoom_res)}var k=$("<div style='position: relative;'>! </div>"),l=this.content_div.width()/f,h;this.content_div.children(":fi rst").remove();this.content_div.append(k),this.max_height=0;var a=Math.floor(i/d/DENSITY);while((a*DENSITY*d)<e){var j=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var c=this.tile_cache.get(j);if(c){var g=a*DENSITY*d;var b=(g-i)*l;if(this.left_offset){b-=this.left_offset}c.css({left:b});k.append(c);this.max_height=Math.max(this.max_height,c.height());this.content_div.css("height",this.max_height+"px")}else{this.delayed_draw(this,j,i,e,a,d,k,l)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height+"px")}}},50)}});var LabelTrack=function(a){Track.call(this,null,a);this.track_type="LabelTrack";this.hidden=true;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($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,a,b){this.track_type="LineTrack";Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.height_px=100;this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={min_value:undefined,max_value:undefined,mode:"Line"};if(b.min_value!==undefined){this.prefs.min_value=b.min_value}if(b.max_value!==undefined){this.prefs.max_value=b.max_value}if(b.mode!==undefined){this.prefs.mode=b.mode}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=unde! fined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null ,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.max_value=data.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;$("#linetrack_"+b+"_minval").remove();$("#linetrack_"+b+"_maxval").remove();var e=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(a.prefs.min_value);var d=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(a.prefs.max_value);d.css({position:"relative",top:"25px",left:"10px"});d.prependTo(a.container_div);e.css({position:"relative",top:a.height_px+55+"px",left:"10px"});e.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=! true;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(p,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*p,a=DENSITY*p,b=$("<canvas class='tile'></canvas>"),v=p+"_"+r;if(this.data_cache.get(v)===undefined){this.get_data(p,r);return}var j=this.data_cache.get(v);if(j===null){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var o=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,n=this.vertical_range,t=this.total_frequency,d=this.height_px,m=this.prefs.mode;o.beginPath();if(data.length>1){var f=Math.ceil((data[1][0]-data[0][0])*e)}else{var f=10}var u,h;for(var q=0;q<data.length;q++){u=(data[q][0]-s)*e;h=data[q][1]! ;if(m=="Intensity"){if(h===null){continue}if(h<=l){h=l}else{if(h>=g){h =g}}h=255-Math.floor((h-l)/n*255);o.fillStyle="rgb("+h+","+h+","+h+")";o.fillRect(u,0,f,this.height_px)}else{if(h===null){if(k&&m==="Filled"){o.lineTo(u,d)}k=false;continue}else{if(h<=l){h=l}else{if(h>=g){h=g}}h=Math.round(d-(h-l)/n*d);if(k){o.lineTo(u,h)}else{k=true;if(m==="Filled"){o.moveTo(u,d);o.lineTo(u,h)}else{o.moveTo(u,h)}}}}}if(m==="Filled"){if(k){o.lineTo(u,d)}o.fill()}else{o.stroke()}c.append(b);return b},gen_options:function(n){var a=$("<div></div>").addClass("form-row");var h="track_"+n+"_minval",k="track_"+n+"_maxval",e="track_"+n+"_mode",l=$("<label></label>").attr("for",h).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),m=$("<input></input>").attr("id",h).val(b),g=$("<label></label>").attr("for",k).text("Max value:"),j=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",k).val(j),d=$("<label></label>").attr("for",e).text("Display mode:"),i=(this.prefs.mode===undefined?"Line":this.prefs.mo! de),c=$('<select id="'+e+'"><option value="Line" id="mode_Line">Line</option><option value="Filled" id="mode_Filled">Filled</option><option value="Intensity" id="mode_Intensity">Intensity</option></select>');c.children("#mode_"+i).attr("selected","selected");return a.append(l).append(m).append(g).append(f).append(d).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_mode option:selected").val();if(a!==this.prefs.min_value||c!==this.prefs.max_value||b!=this.prefs.mode){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.mode=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(c,a,b){this.track_type="FeatureTrack";Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.height_px=100! ;this.container_div.addClass("feature-track");this.dataset_id=a;this.z o_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.default_font="9px Monaco, Lucida Console, monospace";this.left_offset=200;this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.prefs={block_color:"black",label_color:"black",show_counts:false};if(b.block_color!==undefined){this.prefs.block_color=b.block_color}if(b.label_color!==undefined){this.prefs.label_color=b.label_color}if(b.show_counts!==undefined){this.prefs.show_counts=b.show_counts}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.max_low+"_"+a.view.max_high;this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution},function(c){a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=tr! ue;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolution},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,g,c){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=1/a;this.s_e_by_tile[a]={}}var m=this.inc_slots[a].w_scale,v=[],h=0,b=$("<canvas></canvas>").get(0).getContext("2d"),n=this.view.max_low;var d,f,x=[];for(var s=0,t=g.length;s<t;s++){var e=g[s],l=e[0];if(this.inc_slots[a][l]!==undefined){h=Math.max(h,this.inc_slots[a][l]);x.push(this.inc_slots[a][l])}else{v.push(s)}}for(var s=0,t=v.length;s<t;s++){var e=g[v[s]];l=e[0],feature_start=e[1],feature_end=e[2],feature_name=e[3];d=Math.floor((feature_start-n)*m);f=Math.ceil((feature_end-n)*m);if(!c){var p=b.measureText(feature_name).width;if(d-p<0){f+=p}else{d-=p}}var r=0;while(true){var o=true;if(this.s_e_by_tile[a][r]!==undefined){for(var q=0,w=this.s_e_by_tile[a][r].length;q<w;q++){var u=this.s_e_by! _tile[a][r][q];if(f>u[0]&&d<u[1]){o=false;break}}}if(o){if(this.s_e_by _tile[a][r]===undefined){this.s_e_by_tile[a][r]=[]}this.s_e_by_tile[a][r].push([d,f]);this.inc_slots[a][l]=r;h=Math.max(h,r);break}r++}}return h},rect_or_text:function(n,o,g,f,m,b,d,k,e,i){n.textAlign="center";var j=Math.round(o/2);if(d!==undefined&&o>g){n.fillStyle="#555";n.fillRect(k,i+1,e,9);n.fillStyle="#eee";for(var h=0,l=d.length;h<l;h++){if(b+h>=f&&b+h<=m){var a=Math.floor(Math.max(0,(b+h-f)*o));n.fillText(d[h],a+this.left_offset+j,i+9)}}}else{n.fillStyle="#555";n.fillRect(k,i+4,e,3)}},draw_tile:function(W,h,m,ak){var D=h*DENSITY*W,ac=(h+1)*DENSITY*W,C=DENSITY*W;var aj,r;var ad=D+"_"+ac;var w=this.data_cache.get(ad);if(w===undefined){this.data_queue[[D,ac]]=true;this.get_data(D,ac);return}if(w.dataset_type==="summary_tree"){r=30}else{var U=(w.extra_info==="no_detail");var al=(U?this.vertical_nodetail_px:this.vertical_detail_px);r=this.incremental_slots(this.view.zoom_res,w.data,U)*al+15;m.parent().css("height",Math.max(this.height_px,r)+"px");aj=this.inc_slots[this.vi! ew.zoom_res]}var a=Math.ceil(C*ak),K=$("<canvas class='tile'></canvas>"),Y=this.prefs.label_color,f=this.prefs.block_color,O=this.left_offset;K.css({position:"absolute",top:0,left:(D-this.view.low)*ak-O});K.get(0).width=a+O;K.get(0).height=r;var z=K.get(0).getContext("2d"),ah=z.measureText("A").width;z.fillStyle=this.prefs.block_color;z.font=this.default_font;z.textAlign="right";if(w.dataset_type=="summary_tree"){var J,G=55,ab=255-G,g=ab*2/3,Q=w.data,B=w.max,l=w.avg;if(Q.length>2){var b=Math.ceil((Q[1][0]-Q[0][0])*ak)}else{var b=50}for(var af=0,v=Q.length;af<v;af++){var S=Math.ceil((Q[af][0]-D)*ak);var R=Q[af][1];if(!R){continue}J=Math.floor(ab-(R/B)*ab);z.fillStyle="rgb("+J+","+J+","+J+")";z.fillRect(S+O,0,b,20);if(this.prefs.show_counts){if(J>g){z.fillStyle="black"}else{z.fillStyle="#ddd"}z.textAlign="center";z.fillText(Q[af][1],S+O+(b/2),12)}}m.append(K);return K}var ai=w.data;var ae=0;for(var af=0,v=ai.length;af<v;af++){var L=ai[af],I=L[0],ag=L[1],T=L[2],E=L[3];if(ag<=a! c&&T>=D){var V=Math.floor(Math.max(0,(ag-D)*ak)),A=Math.ceil(Math.min( a,Math.max(0,(T-D)*ak))),P=aj[I]*al;if(w.dataset_type==="bai"){z.fillStyle="#555";if(L[4] instanceof Array){var s=Math.floor(Math.max(0,(L[4][0]-D)*ak)),H=Math.ceil(Math.min(a,Math.max(0,(L[4][1]-D)*ak))),q=Math.floor(Math.max(0,(L[5][0]-D)*ak)),o=Math.ceil(Math.min(a,Math.max(0,(L[5][1]-D)*ak)));if(L[4][1]>=D&&L[4][0]<=ac){this.rect_or_text(z,ak,ah,D,ac,L[4][0],L[4][2],s+O,H-s,P)}if(L[5][1]>=D&&L[5][0]<=ac){this.rect_or_text(z,ak,ah,D,ac,L[5][0],L[5][2],q+O,o-q,P)}if(q>H){z.fillStyle="#999";z.fillRect(H+O,P+5,q-H,1)}}else{z.fillStyle="#555";this.rect_or_text(z,ak,ah,D,ac,ag,E,V+O,A-V,P)}if(!U&&ag>D){z.fillStyle=this.prefs.label_color;if(h===0&&V-z.measureText(E).width<0){z.textAlign="left";z.fillText(I,A+2+O,P+8)}else{z.textAlign="right";z.fillText(I,V-2+O,P+8)}z.fillStyle="#555"}}else{if(w.dataset_type==="interval_index"){if(U){z.fillRect(V+O,P+5,A-V,1)}else{var u=L[4],N=L[5],X=L[6],e=L[7];var t,Z,F=null,am=null;if(N&&X){F=Math.floor(Math.max(0,(N-D)*ak));am=Math.ceil(Math! .min(a,Math.max(0,(X-D)*ak)))}if(E!==undefined&&ag>D){z.fillStyle=Y;if(h===0&&V-z.measureText(E).width<0){z.textAlign="left";z.fillText(E,A+2+O,P+8)}else{z.textAlign="right";z.fillText(E,V-2+O,P+8)}z.fillStyle=f}if(e){if(u){if(u=="+"){z.fillStyle=RIGHT_STRAND}else{if(u=="-"){z.fillStyle=LEFT_STRAND}}z.fillRect(V+O,P,A-V,10);z.fillStyle=f}for(var ad=0,d=e.length;ad<d;ad++){var n=e[ad],c=Math.floor(Math.max(0,(n[0]-D)*ak)),M=Math.ceil(Math.min(a,Math.max((n[1]-D)*ak)));if(c>M){continue}t=5;Z=3;z.fillRect(c+O,P+Z,M-c,t);if(F!==undefined&&!(c>am||M<F)){t=9;Z=1;var aa=Math.max(c,F),p=Math.min(M,am);z.fillRect(aa+O,P+Z,p-aa,t)}}}else{t=9;Z=1;z.fillRect(V+O,P+Z,A-V,t);if(L.strand){if(L.strand=="+"){z.fillStyle=RIGHT_STRAND_INV}else{if(L.strand=="-"){z.fillStyle=LEFT_STRAND_INV}}z.fillRect(V+O,P,A-V,10);z.fillStyle=prefs.block_color}}}}}ae++}}m.append(K);return K},gen_options:function(i){var a=$("<div></div>").addClass("form-row");var e="track_"+i+"_block_color",k=$("<label></label! >").attr("for",e).text("Block color:"),l=$("<input></input>").attr("id ",e).attr("name",e).val(this.prefs.block_color),j="track_"+i+"_label_color",g=$("<label></label>").attr("for",j).text("Text color:"),h=$("<input></input>").attr("id",j).attr("name",j).val(this.prefs.label_color),f="track_"+i+"_show_count",c=$("<label></label>").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div></div>").append(b).append(c);return a.append(k).append(l).append(g).append(h).append(d)},update_options:function(d){var b=$("#track_"+d+"_block_color").val(),c=$("#track_"+d+"_label_color").val(),a=$("#track_"+d+"_show_count").attr("checked");if(b!==this.prefs.block_color||c!==this.prefs.label_color||a!=this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=c;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(c,a,b){FeatureTrack.call(this,c,a,b);this.track_type="ReadTrack";this.vertical_det! ail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{}); \ No newline at end of file diff -r e7d91d58f4ad -r 370777a0693f static/scripts/trackster.js --- a/static/scripts/trackster.js Thu May 06 12:11:47 2010 -0400 +++ b/static/scripts/trackster.js Thu May 06 12:30:54 2010 -0400 @@ -5,7 +5,7 @@ var DENSITY = 200, FEATURE_LEVELS = 10, - DATA_ERROR = "There was an error in indexing this dataset.", + DATA_ERROR = "There was an error in indexing this dataset. ", DATA_NOCONVERTER = "A converter for this dataset is not installed. Please check your datatypes_conf.xml file.", DATA_NONE = "No data for this chrom/contig.", DATA_PENDING = "Currently indexing... please wait", @@ -118,17 +118,15 @@ }, remove_track: function( track ) { track.container_div.fadeOut('slow', function() { $(this).remove(); }); - delete this.tracks[track]; + delete this.tracks.splice(this.tracks.indexOf(track)); }, update_options: function() { var sorted = $("ul#sortable-ul").sortable('toArray'); - var payload = []; + for (var id_i in sorted) { + var id = sorted[id_i].split("_li")[0].split("track_")[1]; + $("#viewport").append( $("#track_" + id) ); + } - var divs = $("#viewport > div").sort(function (a, b) { - return sorted.indexOf( $(a).attr('id') ) > sorted.indexOf( $(b).attr('id') ); - }); - $("#viewport > div").remove(); - $("#viewport").html(divs); for (var track_id in view.tracks) { var track = view.tracks[track_id]; if (track.update_options) { @@ -234,13 +232,22 @@ if (track.view.chrom) { $.getJSON( data_url, params, function (result) { - if (!result || result === "error") { + if (!result || result === "error" || result.kind === "error") { track.container_div.addClass("error"); track.content_div.text(DATA_ERROR); + if (result.message) { + var track_id = track.view.tracks.indexOf(track); + var error_link = $("<a href='javascript:void(0);'></a>").attr("id", track_id + "_error"); + error_link.text("Click to view error"); + $("#" + track_id + "_error").live("click", function() { + show_modal( "Trackster Error", "<pre>" + result.message + "</pre>", { "Close" : hide_modal } ); + }); + track.content_div.append(error_link); + } } else if (result === "no converter") { track.container_div.addClass("error"); track.content_div.text(DATA_NOCONVERTER); - } else if (result.data && result.data.length === 0 || result.data === null) { + } else if (result.data !== undefined && (result.data === null || result.data.length === 0)) { track.container_div.addClass("nodata"); track.content_div.text(DATA_NONE); } else if (result === "pending") { @@ -441,7 +448,6 @@ var result = this.data_cache.get(key); if (result === null) { return; } - console.log(result); canvas.css( { position: "absolute", diff -r e7d91d58f4ad -r 370777a0693f templates/tracks/browser.mako --- a/templates/tracks/browser.mako Thu May 06 12:11:47 2010 -0400 +++ b/templates/tracks/browser.mako Thu May 06 12:30:54 2010 -0400 @@ -272,7 +272,6 @@ $.ajax({ url: "${h.url_for( action='chroms' )}", - ## If vis is new, it doesn't have an id, so send the dbkey instead. %if config.get('vis_id'): data: { vis_id: view.vis_id }, %else: @@ -327,7 +326,7 @@ $("#track_" + track_id + "_editable").toggle(); }); del_icon.bind("click", function() { - $("#track_" + track_id + "_li").fadeOut('slow', function() { $("#track_" + track_id).remove(); }); + $("#track_" + track_id + "_li").fadeOut('slow', function() { $("#track_" + track_id + "_li").remove(); }); view.remove_track(track); view.update_options(); }); @@ -354,4 +353,3 @@ </script> </%def> - diff -r e7d91d58f4ad -r 370777a0693f templates/user/dbkeys.mako --- a/templates/user/dbkeys.mako Thu May 06 12:11:47 2010 -0400 +++ b/templates/user/dbkeys.mako Thu May 06 12:30:54 2010 -0400 @@ -41,23 +41,26 @@ <tr class="header"> <th>Name</th> <th>Key</th> - <th>Chroms/Lengths</th> + <th>Number of Chroms</th> <th></th> </tr> % for key, dct in dbkeys.iteritems(): <tr> - <td>${dct["name"] | h}</td> + <td>${dct['name'] | h}</td> <td>${key | h}</td> <td> - <span>${len(dct["chroms"])} entries</span> - <pre id="pre_${key}" class="db_hide"> - <table cellspacing="0" cellpadding="0"> - <tr><th>Chrom</th><th>Length</th></tr> - % for chrom, chrom_len in dct["chroms"].iteritems(): - <tr><td>${chrom | h}</td><td>${chrom_len | h}</td></tr> - % endfor - </table> - </pre> +## <span>${len(dct["chroms"])} entries</span> +## <pre id="pre_${key}" class="db_hide"> +## <table cellspacing="0" cellpadding="0"> +## <tr><th>Chrom</th><th>Length</th></tr> +## % for chrom, chrom_len in dct["chroms"].iteritems(): +## <tr><td>${chrom | h}</td><td>${chrom_len | h}</td></tr> +## % endfor +## </table> +## </pre> + % if 'count' in dct: + ${dct['count']} + % endif </td> <td><form action="dbkeys" method="post"><input type="hidden" name="key" value="${key}" /><input type="submit" name="delete" value="Delete" /></form></td> </tr> diff -r e7d91d58f4ad -r 370777a0693f tool_conf.xml.main --- a/tool_conf.xml.main Thu May 06 12:11:47 2010 -0400 +++ b/tool_conf.xml.main Thu May 06 12:30:54 2010 -0400 @@ -35,6 +35,7 @@ <tool file="filters/changeCase.xml" /> <tool file="filters/pasteWrapper.xml" /> <tool file="filters/remove_beginning.xml" /> + <tool file="filters/randomlines.xml" /> <tool file="filters/headWrapper.xml" /> <tool file="filters/tailWrapper.xml" /> <tool file="filters/trimmer.xml" />

1 0

[hg] galaxy 3749: Updated builds.txt (and manual_builds.txt) to ...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/e7d91d58f4ad changeset: 3749:e7d91d58f4ad user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Thu May 06 12:11:47 2010 -0400 description: Updated builds.txt (and manual_builds.txt) to newest version, corresponding to that on main. Includes hg19 and phiX correction. diffstat: tool-data/shared/ucsc/builds.txt | 291 +++++++++++++++++-------------- tool-data/shared/ucsc/manual_builds.txt | 2 +- 2 files changed, 160 insertions(+), 133 deletions(-) diffs (355 lines): diff -r 91bc27508c75 -r e7d91d58f4ad tool-data/shared/ucsc/builds.txt --- a/tool-data/shared/ucsc/builds.txt Thu May 06 10:58:23 2010 -0400 +++ b/tool-data/shared/ucsc/builds.txt Thu May 06 12:11:47 2010 -0400 @@ -1,133 +1,156 @@ #Harvested from http://genome-test.cse.ucsc.edu/cgi-bin/das/dsn ? unspecified (?) -hg18 Human Mar. 2006 (hg18) -hg17 Human May 2004 (hg17) -hg16 Human July 2003 (hg16) -hg15 Human Apr. 2003 (hg15) -hg13 Human Nov. 2002 (hg13) -venter1 J. Craig Venter Sep. 2007 (venter1) -panTro2 Chimp Mar. 2006 (panTro2) -panTro1 Chimp Nov. 2003 (panTro1) -ponAbe2 Orangutan July 2007 (ponAbe2) -rheMac2 Rhesus Jan. 2006 (rheMac2) -calJac1 Marmoset June 2007 (calJac1) -otoGar1 Bushbaby Dec. 2006 (otoGar1) -tupBel1 TreeShrew Dec. 2006 (tupBel1) -mm9 Mouse July 2007 (mm9) -mm8 Mouse Feb. 2006 (mm8) -mm7 Mouse Aug. 2005 (mm7) -mm6 Mouse Mar. 2005 (mm6) -mm5 Mouse May 2004 (mm5) -mm4 Mouse Oct. 2003 (mm4) -mm3 Mouse Feb. 2003 (mm3) -mm2 Mouse Feb. 2002 (mm2) -rn4 Rat Nov. 2004 (rn4) -rn3 Rat June 2003 (rn3) -rn2 Rat Jan. 2003 (rn2) -oryCun1 Rabbit May 2005 (oryCun1) -felCat3 Cat Mar. 2006 (felCat3) -canFam2 Dog May 2005 (canFam2) -canFam1 Dog July 2004 (canFam1) -equCab1 Horse Jan. 2007 (equCab1) -bosTau4 Cow Oct. 2007 (bosTau4) -bosTau3 Cow Aug. 2006 (bosTau3) -bosTau2 Cow Mar. 2005 (bosTau2) -bosTau1 Cow Sep. 2004 (bosTau1) -choHof1 Sloth Feb. 2008 (choHof1) -dasNov1 Armadillo May 2005 (dasNov1) -echTel1 Tenrec July 2005 (echTel1) -loxAfr1 Elephant May 2005 (loxAfr1) -monDom4 Opossum Jan. 2006 (monDom4) -monDom1 Opossum Oct. 2004 (monDom1) -ornAna1 Platypus Mar. 2007 (ornAna1) -galGal3 Chicken May 2006 (galGal3) -galGal2 Chicken Feb. 2004 (galGal2) -anoCar1 Lizard Feb. 2007 (anoCar1) -xenTro2 X. tropicalis Aug. 2005 (xenTro2) -xenTro1 X. tropicalis Oct. 2004 (xenTro1) -danRer5 Zebrafish July 2007 (danRer5) -danRer4 Zebrafish Mar. 2006 (danRer4) -danRer3 Zebrafish May 2005 (danRer3) -danRer2 Zebrafish June 2004 (danRer2) -danRer1 Zebrafish Nov. 2003 (danRer1) -tetNig1 Tetraodon Feb. 2004 (tetNig1) -fr2 Fugu Oct. 2004 (fr2) -fr1 Fugu Aug. 2002 (fr1) -gasAcu1 Stickleback Feb. 2006 (gasAcu1) -oryLat1 Medaka Apr. 2006 (oryLat1) -petMar1 Lamprey Mar. 2007 (petMar1) -borEut13 Boreoeutherian Apr. 24. 2006 (borEut13) -canHg12 Boreoeutherian Nov. 19. 2005 (canHg12) -rodEnt13 Rodent Apr. 24. 2006 (rodEnt13) -priMat13 Primate Apr. 24. 2006 (priMat13) -nonAfr13 Non-Afrotheria Apr. 24. 2006 (nonAfr13) -lauRas13 Laurasiatheria Apr. 24. 2006 (lauRas13) -homIni14 Hominidae Oct. 1. 2006 (homIni14) -homIni13 Hominidae Apr. 24. 2006 (homIni13) -gliRes13 Glires Apr. 24. 2006 (gliRes13) -eutHer13 Eutheria Apr. 24. 2006 (eutHer13) -euaGli13 Euarchontoglires Apr. 24. 2006 (euaGli13) -catArr1 Catarrhini June 13. 2006 (catArr1) -afrOth13 Afrotheria Apr. 24. 2006 (afrOth13) -braFlo1 Lancelet Mar. 2006 (braFlo1) -ci2 C. intestinalis Mar. 2005 (ci2) -ci1 C. intestinalis Dec. 2002 (ci1) -cioSav2 C. savignyi July 2005 (cioSav2) -cioSav1 C. savignyi Sept. 2001 (cioSav1) -strPur2 S. purpuratus Sep. 2006 (strPur2) -strPur1 S. purpuratus Apr. 2005 (strPur1) -ce4 C. elegans Jan. 2007 (ce4) -ce3 C. elegans March 2005 (ce3) -ce2 C. elegans Mar. 2004 (ce2) -ce1 C. elegans May 2003 (ce1) -caePb1 C. brenneri Jan. 2007 (caePb1) -cb3 C. briggsae Jan. 2007 (cb3) -cb2 C. briggsae Aug 2005 (cb2) -cb1 C. briggsae July 2002 (cb1) -caeRem2 C. remanei Mar. 2006 (caeRem2) -caeRem1 C. remanei March 2005 (caeRem1) -priPac1 P. pacificus Feb. 2007 (priPac1) -dm3 D. melanogaster Apr. 2006 (dm3) -dm2 D. melanogaster Apr. 2004 (dm2) -dm1 D. melanogaster Jan. 2003 (dm1) -droSim1 D. simulans Apr. 2005 (droSim1) -droSec1 D. sechellia Oct. 2005 (droSec1) -droYak2 D. yakuba Nov. 2005 (droYak2) -droYak1 D. yakuba Apr. 2004 (droYak1) -droEre1 D. erecta Aug. 2005 (droEre1) -droAna2 D. ananassae Aug. 2005 (droAna2) -droAna1 D. ananassae July 2004 (droAna1) -dp3 D. pseudoobscura Nov. 2004 (dp3) -dp2 D. pseudoobscura Aug. 2003 (dp2) -droPer1 D. persimilis Oct. 2005 (droPer1) -droVir2 D. virilis Aug. 2005 (droVir2) -droVir1 D. virilis July 2004 (droVir1) -droMoj2 D. mojavensis Aug. 2005 (droMoj2) -droMoj1 D. mojavensis Aug. 2004 (droMoj1) -droGri1 D. grimshawi Aug. 2005 (droGri1) -anoGam1 A. gambiae Feb. 2003 (anoGam1) -apiMel2 A. mellifera Jan. 2005 (apiMel2) -apiMel1 A. mellifera July 2004 (apiMel1) -triCas2 T. castaneum Sep. 2005 (triCas2) -falciparum P. falciparum Plasmodium falciparum (falciparum) -sacCer1 S. cerevisiae Oct. 2003 (sacCer1) -sc1 SARS coronavirus Apr. 2003 (sc1) -campJeju1 Campylobacter jejuni 02/25/2000 (campJeju1) -campJeju_RM1221_1 Campylobacter jejuni RM1221 01/07/2005 (campJeju_RM1221_1) -eschColi_CFT073_1 Escherichia coli CFT073 12/10/2002 (eschColi_CFT073_1) -eschColi_K12_1 Escherichia coli K12 09/05/1997 (eschColi_K12_1) -eschColi_O157H7_1 Escherichia coli O157H7 03/29/2000 (eschColi_O157H7_1) -eschColi_O157H7EDL933_1 Escherichia coli O157H7 EDL933 02/24/2001 (eschColi_O157H7EDL933_1) -vibrChol1 Vibrio cholerae O1 El Tor 08/22/2000 (vibrChol1) -vibrChol_MO10_1 Vibrio cholerae MO10 09/17/2005 (vibrChol_MO10_1) -vibrChol_O395_1 Vibrio cholerae O395 09/17/2005 (vibrChol_O395_1) -vibrFisc_ES114_1 Vibrio fischeri ES114 02/11/2005 (vibrFisc_ES114_1) -vibrPara1 Vibrio parahaemolyticus 06/02/2000 (vibrPara1) -vibrVuln_CMCP6_1 Vibrio vulnificus CMCP6 09/23/2003 (vibrVuln_CMCP6_1) -vibrVuln_YJ016_1 Vibrio vulnificus YJ016 12/06/2003 (vibrVuln_YJ016_1) -heliHepa1 Helicobacter hepaticus 06/18/2003 (heliHepa1) -heliPylo_26695_1 Helicobacter pylori 26695 08/07/1997 (heliPylo_26695_1) -heliPylo_J99_1 Helicobacter pylori J99 01/29/1999 (heliPylo_J99_1) +hg19Haps hg19Haplotypes Feb. 2009 (GRCh37/hg19Haps) (hg19Haps) +hg19 Human Feb. 2009 (GRCh37/hg19) (hg19) +hg18 Human Mar. 2006 (NCBI36/hg18) (hg18) +hg17 Human May 2004 (NCBI35/hg17) (hg17) +hg16 Human July 2003 (NCBI34/hg16) (hg16) +hg15 Human Apr. 2003 (NCBI33/hg15) (hg15) +venter1 J. Craig Venter Sep. 2007 (HuRef/venter1) (venter1) +panTro2 Chimp Mar. 2006 (CGSC 2.1/panTro2) (panTro2) +panTro1 Chimp Nov. 2003 (CGSC 1.1/panTro1) (panTro1) +gorGor2 Gorilla Aug. 2009 (Sanger 4/gorGor2) (gorGor2) +gorGor1 Gorilla Oct. 2008 (Sanger 0.1/gorGor1) (gorGor1) +ponAbe2 Orangutan July 2007 (WUGSC 2.0.2/ponAbe2) (ponAbe2) +rheMac2 Rhesus Jan. 2006 (MGSC Merged 1.0/rheMac2) (rheMac2) +papHam1 Baboon Nov. 2008 (Baylor 1.0/papHam1) (papHam1) +calJac3 Marmoset March 2009 (WUGSC 3.2/calJac3) (calJac3) +calJac1 Marmoset June 2007 (WUGSC 2.0.2/calJac1) (calJac1) +otoGar1 Bushbaby Dec. 2006 (Broad/otoGar1) (otoGar1) +micMur1 Mouse lemur Jun. 2003 (Broad/micMur1) (micMur1) +tupBel1 Tree shrew Dec. 2006 (Broad/tupBel1) (tupBel1) +mmtv MMTV Nov. 2009 (MMTV/mmtv) (mmtv) +homPan20 chimp/human Jun. 2008 (UCSC Recon/homPan20) (homPan20) +homIni20 orang/human Jun. 2008 (UCSC Recon/homIni20) (homIni20) +sorAra1 Shrew June 2006 (Broad/sorAra1) (sorAra1) +mm9 Mouse July 2007 (NCBI37/mm9) (mm9) +mm8 Mouse Feb. 2006 (NCBI36/mm8) (mm8) +mm7 Mouse Aug. 2005 (NCBI35/mm7) (mm7) +rn4 Rat Nov. 2004 (Baylor 3.4/rn4) (rn4) +rn3 Rat June 2003 (Baylor 3.1/rn3) (rn3) +speTri1 Squirrel Feb. 2008 (Broad/speTri1) (speTri1) +cavPor3 Guinea pig Feb. 2008 (Broad/cavPor3) (cavPor3) +oryCun2 Rabbit Apr. 2009 (Broad/oryCun2) (oryCun2) +oryCun1 Rabbit May 2005 (Broad/oryCun1) (oryCun1) +ochPri2 Pika Jul. 2008 (Broad/ochPri2) (ochPri2) +eriEur1 Hedgehog June 2006 (Broad/eriEur1) (eriEur1) +felCatV17e Cat Dec. 2008 (NHGRI/GTB V17e/felCatV17e) (felCatV17e) +felCat3 Cat Mar. 2006 (Broad/felCat3) (felCat3) +ailMel1 Panda Dec. 2009 (BGI-Shenzhen 1.0/ailMel1) (ailMel1) +nemVec1 Starlet sea anemone Jun. 2007 (JGI-PDF/nemVec1) (nemVec1) +canFam2 Dog May 2005 (Broad/canFam2) (canFam2) +canFam1 Dog July 2004 (Broad/canFam1) (canFam1) +canFamPoodle1 Dog May 2003 (TIGR Poodle/canFamPoodle1) (canFamPoodle1) +equCab2 Horse Sep. 2007 (Broad/equCab2) (equCab2) +equCab1 Horse Jan. 2007 (Broad/equCab1) (equCab1) +susScr2 Pig Nov. 2009 (SGSC Sscrofa9.2/susScr2) (susScr2) +pteVam1 Megabat Jul. 2008 (Broad/pteVam1) (pteVam1) +myoLuc1 Microbat Mar. 2006 (Broad/myoLuc1) (myoLuc1) +susScr1 Pig Apr. 2009 (SGSC 9.53/susScr1) (susScr1) +turTru1 Dolphin Feb. 2008 (Broad/turTru1) (turTru1) +tarSyr1 Tarsier Aug. 2008 (Broad/tarSyr1) (tarSyr1) +proCap1 Rock hyrax Jul. 2008 (Broad/proCap1) (proCap1) +oviAri1 Sheep Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1) (oviAri1) +dipOrd1 Kangaroo rat Jul. 2008 (Broad/dipOrd1) (dipOrd1) +choHof1 Sloth Jul. 2008 (Broad/choHof1) (choHof1) +bosTau4 Cow Oct. 2007 (Baylor 4.0/bosTau4) (bosTau4) +bosTau3 Cow Aug. 2006 (Baylor 3.1/bosTau3) (bosTau3) +bosTau2 Cow Mar. 2005 (Baylor 2.0/bosTau2) (bosTau2) +macEug1 Wallaby Nov. 2007 (Baylor 1.0/macEug1) (macEug1) +dasNov2 Armadillo Jul. 2008 (Broad/dasNov2) (dasNov2) +dasNov1 Armadillo May 2005 (Broad/dasNov1) (dasNov1) +echTel1 Tenrec July 2005 (Broad/echTel1) (echTel1) +loxAfr3 Elephant Jul. 2009 (Broad/loxAfr3) (loxAfr3) +loxAfr2 Elephant Jul. 2008 (Broad/loxAfr2) (loxAfr2) +loxAfr1 Elephant May 2005 (Broad/loxAfr1) (loxAfr1) +monDom5 Opossum Oct. 2006 (Broad/monDom5) (monDom5) +monDom4 Opossum Jan. 2006 (Broad/monDom4) (monDom4) +monDom1 Opossum Oct. 2004 (Broad prelim/monDom1) (monDom1) +ornAna1 Platypus Mar. 2007 (WUGSC 5.0.1/ornAna1) (ornAna1) +galGal3 Chicken May 2006 (WUGSC 2.1/galGal3) (galGal3) +galGal2 Chicken Feb. 2004 (WUGSC 1.0/galGal2) (galGal2) +taeGut1 Zebra finch Jul. 2008 (WUGSC 3.2.4/taeGut1) (taeGut1) +anoCar1 Lizard Feb. 2007 (Broad/anoCar1) (anoCar1) +xenTro2 X. tropicalis Aug. 2005 (JGI 4.1/xenTro2) (xenTro2) +xenTro1 X. tropicalis Oct. 2004 (JGI 3.0/xenTro1) (xenTro1) +danRer6 Zebrafish Dec. 2008 (Zv8/danRer6) (danRer6) +danRer5 Zebrafish July 2007 (Zv7/danRer5) (danRer5) +danRer4 Zebrafish Mar. 2006 (Zv6/danRer4) (danRer4) +danRer3 Zebrafish May 2005 (Zv5/danRer3) (danRer3) +tetNig2 Tetraodon Mar. 2007 (Genoscope 8.0/tetNig2) (tetNig2) +tetNig1 Tetraodon Feb. 2004 (Genoscope 7/tetNig1) (tetNig1) +fr2 Fugu Oct. 2004 (JGI 4.0/fr2) (fr2) +fr1 Fugu Aug. 2002 (JGI 3.0/fr1) (fr1) +gasAcu1 Stickleback Feb. 2006 (Broad/gasAcu1) (gasAcu1) +oryLat2 Medaka Oct. 2005 (NIG/UT MEDAKA1/oryLat2) (oryLat2) +oryLat1 Medaka Apr. 2006 (NIG/UT MEDAKA1/oryLat1) (oryLat1) +petMar1 Lamprey Mar. 2007 (WUGSC 3.0/petMar1) (petMar1) +borEut13 Boreoeutherian Apr. 24. 2006 (UCSC Recon/borEut13) (borEut13) +canHg12 Boreoeutherian Nov. 19. 2005 (UCSC Recon/canHg12) (canHg12) +rodEnt13 Rodent Apr. 24. 2006 (UCSC Recon/rodEnt13) (rodEnt13) +priMat13 Primate Apr. 24. 2006 (UCSC Recon/priMat13) (priMat13) +nonAfr13 Non-Afrotheria Apr. 24. 2006 (UCSC Recon/nonAfr13) (nonAfr13) +lauRas13 Laurasiatheria Apr. 24. 2006 (UCSC Recon/lauRas13) (lauRas13) +homIni14 Hominidae Oct. 1. 2006 (UCSC Recon/homIni14) (homIni14) +homIni13 Hominidae Apr. 24. 2006 (UCSC Recon/homIni13) (homIni13) +gliRes13 Glires Apr. 24. 2006 (UCSC Recon/gliRes13) (gliRes13) +eutHer13 Eutheria Apr. 24. 2006 (UCSC Recon/eutHer13) (eutHer13) +euaGli13 Euarchontoglires Apr. 24. 2006 (UCSC Recon/euaGli13) (euaGli13) +catArr1 Catarrhini June 13. 2006 (UCSC Recon/catArr1) (catArr1) +afrOth13 Afrotheria Apr. 24. 2006 (UCSC Recon/afrOth13) (afrOth13) +braFlo1 Lancelet Mar. 2006 (JGI 1.0/braFlo1) (braFlo1) +ci2 C. intestinalis Mar. 2005 (JGI 2.1/ci2) (ci2) +ci1 C. intestinalis Dec. 2002 (JGI 1.0/ci1) (ci1) +cioSav2 C. savignyi July 2005 (Sidow Lab 2.0/cioSav2) (cioSav2) +cioSav1 C. savignyi Apr. 2003 (Broad/cioSav1) (cioSav1) +strPur2 S. purpuratus Sep. 2006 (Baylor 2.1/strPur2) (strPur2) +strPur1 S. purpuratus Apr. 2005 (Baylor 1.1/strPur1) (strPur1) +ce8 C. elegans Jun 2009 (WS204/ce8) (ce8) +ce7 C. elegans Feb 2009 (WS200/ce7) (ce7) +aplCal1 Sea hare Sept. 2008 (Broad 2.0/aplCal1) (aplCal1) +ce6 C. elegans May 2008 (WS190/ce6) (ce6) +ce5 C. elegans Aug. 2007 (WS180/ce5) (ce5) +ce4 C. elegans Jan. 2007 (WS170/ce4) (ce4) +ce3 C. elegans March 2005 (WS140/ce3) (ce3) +ce2 C. elegans Mar. 2004 (WS120/ce2) (ce2) +caePb2 C. brenneri Feb. 2008 (WUGSC 6.0.1/caePb2) (caePb2) +caePb1 C. brenneri Jan. 2007 (WUGSC 4.0/caePb1) (caePb1) +cb3 C. briggsae Jan. 2007 (WUGSC 1.0/cb3) (cb3) +cb2 C. briggsae Aug 2005 (WUGSC prelim/cb2) (cb2) +cb1 C. briggsae July 2002 (WormBase cb25.agp8/cb1) (cb1) +caeRem3 C. remanei May 2007 (WUGSC 15.0.1/caeRem3) (caeRem3) +caeRem2 C. remanei Mar. 2006 (WUGSC 1.0/caeRem2) (caeRem2) +caeRem1 C. remanei March 2005 (WUGSC prelim/caeRem1) (caeRem1) +caeJap2 C. japonica Jan. 2009 (WUGSC 4.0.1/caeJap2) (caeJap2) +caeJap1 C. japonica Mar. 2008 (WUGSC 3.0.2/caeJap1) (caeJap1) +priPac1 P. pacificus Feb. 2007 (WUGSC 5.0/priPac1) (priPac1) +dm3 D. melanogaster Apr. 2006 (BDGP R5/dm3) (dm3) +dm2 D. melanogaster Apr. 2004 (BDGP R4/dm2) (dm2) +dm1 D. melanogaster Jan. 2003 (BDGP R3/dm1) (dm1) +droSim1 D. simulans Apr. 2005 (WUGSC mosaic 1.0/droSim1) (droSim1) +droSec1 D. sechellia Oct. 2005 (Broad/droSec1) (droSec1) +droYak2 D. yakuba Nov. 2005 (WUGSC 7.1/droYak2) (droYak2) +droYak1 D. yakuba Apr. 2004 (WUGSC 1.0/droYak1) (droYak1) +droEre1 D. erecta Aug. 2005 (Agencourt prelim/droEre1) (droEre1) +droAna2 D. ananassae Aug. 2005 (Agencourt prelim/droAna2) (droAna2) +droAna1 D. ananassae July 2004 (TIGR/droAna1) (droAna1) +dp3 D. pseudoobscura Nov. 2004 (FlyBase 1.03/dp3) (dp3) +dp2 D. pseudoobscura Aug. 2003 (Baylor freeze1/dp2) (dp2) +droPer1 D. persimilis Oct. 2005 (Broad/droPer1) (droPer1) +droVir2 D. virilis Aug. 2005 (Agencourt prelim/droVir2) (droVir2) +droVir1 D. virilis July 2004 (Agencourt prelim/droVir1) (droVir1) +droMoj2 D. mojavensis Aug. 2005 (Agencourt prelim/droMoj2) (droMoj2) +droMoj1 D. mojavensis Aug. 2004 (Agencourt prelim/droMoj1) (droMoj1) +droGri1 D. grimshawi Aug. 2005 (Agencourt prelim/droGri1) (droGri1) +anoGam1 A. gambiae Feb. 2003 (IAGEC MOZ2/anoGam1) (anoGam1) +apiMel2 A. mellifera Jan. 2005 (Baylor 2.0/apiMel2) (apiMel2) +apiMel1 A. mellifera July 2004 (Baylor 1.2/apiMel1) (apiMel1) +triCas2 T. castaneum Sep. 2005 (Baylor 2.0/triCas2) (triCas2) +falciparum P. falciparum Plasmodium falciparum (?/falciparum) (falciparum) +sacCer2 S. cerevisiae June 2008 (SGD/sacCer2) (sacCer2) +sacCer1 S. cerevisiae Oct. 2003 (SGD/sacCer1) (sacCer1) +sc1 SARS coronavirus Apr. 2003 (GenBank Apr. 14 '03/sc1) (sc1) +phiX phiX174 (phiX) 16079 Mycobacterium sp. JLS (16079) symbTher_IAM14863 Symbiobacterium thermophilum IAM 14863 (symbTher_IAM14863) 16070 Yersinia pseudotuberculosis IP 31758 (16070) @@ -356,6 +379,7 @@ 16062 Leuconostoc citreum KM20 (16062) 16148 Leptospira borgpetersenii serovar Hardjo-bovis JB197 (16148) 16146 Leptospira borgpetersenii serovar Hardjo-bovis L550 (16146) +vibrVuln_CMCP6_1 Vibrio vulnificus CMCP6 (vibrVuln_CMCP6_1) 10877 Bacillus thuringiensis serovar konkukian str. 97-27 (10877) 19517 Clostridium botulinum A str. ATCC 19397 (19517) nitrWino_NB_255 Nitrobacter winogradskyi Nb-255 (nitrWino_NB_255) @@ -500,6 +524,7 @@ 28507 Clostridium botulinum A3 str. Loch Maree (28507) colwPsyc_34H Colwellia psychrerythraea 34H (colwPsyc_34H) hyphNept_ATCC15444 Hyphomonas neptunium ATCC 15444 (hyphNept_ATCC15444) +vibrChol1 Vibrio cholerae O1 biovar eltor str. N16961 (vibrChol1) deinGeot_DSM11300 Deinococcus geothermalis DSM 11300 (deinGeot_DSM11300) 312 Buchnera aphidicola str. Sg (Schizaphis graminum) (312) 311 Streptococcus pyogenes MGAS315 (311) @@ -536,6 +561,7 @@ 12720 Enterobacter sakazakii ATCC BAA-894 (12720) therMari Thermotoga maritima MSB8 (therMari) mycoGeni Mycoplasma genitalium G37 (mycoGeni) +vibrFisc_ES114_1 Vibrio fischeri ES114 (vibrFisc_ES114_1) pyroIsla1 Pyrobaculum islandicum DSM 4184 (pyroIsla1) 17407 Burkholderia multivorans ATCC 17616 (17407) 13030 Salmonella enterica subsp. arizonae serovar 62:z4,z23:-- (13030) @@ -544,6 +570,7 @@ 19857 Vibrio harveyi ATCC BAA-1116 (19857) 17639 Parvibaculum lavamentivorans DS-1 (17639) 18059 Mycobacterium bovis BCG str. Pasteur 1173P2 (18059) +vibrPara1 Vibrio parahaemolyticus RIMD 2210633 (vibrPara1) 259 Escherichia coli O157:H7 EDL933 (259) 64 Staphylococcus epidermidis RP62A (64) neisGono_FA1090_1 Neisseria gonorrhoeae FA 1090 (neisGono_FA1090_1) @@ -598,6 +625,7 @@ vermEise_EF01_2 Verminephrobacter eiseniae EF01-2 (vermEise_EF01_2) granBeth_CGDNIH1 Granulibacter bethesdensis CGDNIH1 (granBeth_CGDNIH1) alcaBork_SK2 Alcanivorax borkumensis SK2 (alcaBork_SK2) +vibrChol_O395_1 Vibrio cholerae O395 (vibrChol_O395_1) nitrOcea_ATCC19707 Nitrosococcus oceani ATCC 19707 (nitrOcea_ATCC19707) campJeju_RM1221 Campylobacter jejuni RM1221 (campJeju_RM1221) 12468 Bacillus cereus E33L (12468) @@ -723,6 +751,7 @@ 12637 Clostridium beijerinckii NCIMB 8052 (12637) ehrlRumi_WELGEVONDEN Ehrlichia ruminantium str. Welgevonden (ehrlRumi_WELGEVONDEN) methLabrZ_1 Methanocorpusculum labreanum Z (methLabrZ_1) +vibrVuln_YJ016_1 Vibrio vulnificus YJ016 (vibrVuln_YJ016_1) 13773 Streptococcus thermophilus LMD-9 (13773) 20039 Leptothrix cholodnii SP-6 (20039) shewAmaz Shewanella amazonensis SB2B (shewAmaz) @@ -786,7 +815,5 @@ aeroHydr_ATCC7966 Aeromonas hydrophila subsp. hydrophila ATCC 7966 (aeroHydr_ATCC7966) baciAnth_AMES Bacillus anthracis str. Ames (baciAnth_AMES) shewOnei Shewanella oneidensis MR-1 (shewOnei) -equCab2 Horse Sep. 2007 (equCab2) -arabidopsis Arabidopsis thaliana TAIR9 -arabidopsis_tair8 Arabidopsis thaliana TAIR8 -araTha1 Arabidopsis thaliana TAIR7 +15217 Human herpesvirus 1 (15217) +lMaj5 Leishmania major 2005 (lMaj5) diff -r 91bc27508c75 -r e7d91d58f4ad tool-data/shared/ucsc/manual_builds.txt --- a/tool-data/shared/ucsc/manual_builds.txt Thu May 06 10:58:23 2010 -0400 +++ b/tool-data/shared/ucsc/manual_builds.txt Thu May 06 12:11:47 2010 -0400 @@ -1,4 +1,4 @@ -phix phiX174 phix=5386 +phiX phiX174 phiX=5386 16079 Mycobacterium sp. JLS NC_009077=6048425 symbTher_IAM14863 Symbiobacterium thermophilum IAM 14863 chr=3566135 16070 Yersinia pseudotuberculosis IP 31758 NC_009708=4723306,NC_009705=153140,NC_009704=58679

1 0

[hg] galaxy 3748: Update documentation in cufftools wrappers.
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/91bc27508c75 changeset: 3748:91bc27508c75 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Thu May 06 10:58:23 2010 -0400 description: Update documentation in cufftools wrappers. diffstat: tools/ngs_rna/cuffcompare_wrapper.xml | 2 +- tools/ngs_rna/cuffdiff_wrapper.xml | 26 +++++++++++++++++++------- tools/ngs_rna/cufflinks_wrapper.xml | 2 +- 3 files changed, 21 insertions(+), 9 deletions(-) diffs (76 lines): diff -r e72342f71adc -r 91bc27508c75 tools/ngs_rna/cuffcompare_wrapper.xml --- a/tools/ngs_rna/cuffcompare_wrapper.xml Thu May 06 10:43:13 2010 -0400 +++ b/tools/ngs_rna/cuffcompare_wrapper.xml Thu May 06 10:58:23 2010 -0400 @@ -93,7 +93,7 @@ <help> **Cuffcompare Overview** -Cuffcompare is part of Cufflinks_. Cuffcompare helps you: (a) compare your assembled transcripts to a reference annotation and (b) track Cufflinks transcripts across multiple experiments (e.g. across a time course). Please cite: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. (manuscript in press) +Cuffcompare is part of Cufflinks_. Cuffcompare helps you: (a) compare your assembled transcripts to a reference annotation and (b) track Cufflinks transcripts across multiple experiments (e.g. across a time course). Please cite: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nature Biotechnology doi:10.1038/nbt.1621 .. _Cufflinks: http://cufflinks.cbcb.umd.edu/ diff -r e72342f71adc -r 91bc27508c75 tools/ngs_rna/cuffdiff_wrapper.xml --- a/tools/ngs_rna/cuffdiff_wrapper.xml Thu May 06 10:43:13 2010 -0400 +++ b/tools/ngs_rna/cuffdiff_wrapper.xml Thu May 06 10:58:23 2010 -0400 @@ -48,13 +48,13 @@ <data format="tabular" name="genes_exp" label="${tool.name} on ${on_string}: gene expression"/> <data format="tabular" name="tss_groups_exp" label="${tool.name} on ${on_string}: TSS groups expression"/> <data format="tabular" name="cds_exp_fpkm_tracking" label="${tool.name} on ${on_string}: CDS Expression FPKM Tracking"/> - <data format="tabular" name="splicing_diff" label="${tool.name} on ${on_string}: splicing diff"/> - <data format="tabular" name="cds_diff" label="${tool.name} on ${on_string}: CDS diff"/> - <data format="tabular" name="promoters_diff" label="${tool.name} on ${on_string}: promoters diff"/> + <data format="tabular" name="isoforms_fpkm_tracking" label="${tool.name} on ${on_string}: isoform FPKM tracking"/> + <data format="tabular" name="genes_fpkm_tracking" label="${tool.name} on ${on_string}: gene FPKM tracking"/> <data format="tabular" name="tss_groups_fpkm_tracking" label="${tool.name} on ${on_string}: TSS groups FPKM tracking" /> <data format="tabular" name="cds_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM tracking"/> - <data format="tabular" name="genes_fpkm_tracking" label="${tool.name} on ${on_string}: gene FPKM tracking"/> - <data format="tabular" name="isoforms_fpkm_tracking" label="${tool.name} on ${on_string}: isoform FPKM tracking"/> + <data format="tabular" name="splicing_diff" label="${tool.name} on ${on_string}: splicing diff"/> + <data format="tabular" name="promoters_diff" label="${tool.name} on ${on_string}: promoters diff"/> + <data format="tabular" name="cds_diff" label="${tool.name} on ${on_string}: CDS diff"/> </outputs> <tests> @@ -65,7 +65,7 @@ <help> **Cuffdiff Overview** -Cuffdiff is part of Cufflinks_. Cuffdiff find significant changes in transcript expression, splicing, and promoter use. Please cite: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. (manuscript in press) +Cuffdiff is part of Cufflinks_. Cuffdiff find significant changes in transcript expression, splicing, and promoter use. Please cite: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nature Biotechnology doi:10.1038/nbt.1621 .. _Cufflinks: http://cufflinks.cbcb.umd.edu/ @@ -91,7 +91,19 @@ **Outputs** -TODO +Cuffdiff produces many output files: + +1. Transcript FPKM expression tracking. +2. Gene FPKM expression tracking; tracks the summed FPKM of transcripts sharing each gene_id +3. Primary transcript FPKM tracking; tracks the summed FPKM of transcripts sharing each tss_id +4. Coding sequence FPKM tracking; tracks the summed FPKM of transcripts sharing each p_id, indepedent of tss_id +5. Transcript differential FPKM. +6. Gene differential FPKM. Tests difference sin the summed FPKM of transcripts sharing each gene_id +7. Primary transcript differential FPKM. Tests difference sin the summed FPKM of transcripts sharing each tss_id +8. Coding sequence differential FPKM. Tests difference sin the summed FPKM of transcripts sharing each p_id independent of tss_id +9. Differential splicing tests: this tab delimited file lists, for each primary transcript, the amount of overloading detected among its isoforms, i.e. how much differential splicing exists between isoforms processed from a single primary transcript. Only primary transcripts from which two or more isoforms are spliced are listed in this file. +10. Differential promoter tests: this tab delimited file lists, for each gene, the amount of overloading detected among its primary transcripts, i.e. how much differential promoter use exists between samples. Only genes producing two or more distinct primary transcripts (i.e. multi-promoter genes) are listed here. +11. Differential CDS tests: this tab delimited file lists, for each gene, the amount of overloading detected among its coding sequences, i.e. how much differential CDS output exists between samples. Only genes producing two or more distinct CDS (i.e. multi-protein genes) are listed here. ------- diff -r e72342f71adc -r 91bc27508c75 tools/ngs_rna/cufflinks_wrapper.xml --- a/tools/ngs_rna/cufflinks_wrapper.xml Thu May 06 10:43:13 2010 -0400 +++ b/tools/ngs_rna/cufflinks_wrapper.xml Thu May 06 10:58:23 2010 -0400 @@ -77,7 +77,7 @@ <help> **Cufflinks Overview** -Cufflinks_ assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one. Please cite: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. (manuscript in press) +Cufflinks_ assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one. Please cite: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nature Biotechnology doi:10.1038/nbt.1621 .. _Cufflinks: http://cufflinks.cbcb.umd.edu/

1 0

[hg] galaxy 3747: lims: workflow selectbox in the samples page f...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/e72342f71adc changeset: 3747:e72342f71adc user: rc date: Thu May 06 10:43:13 2010 -0400 description: lims: workflow selectbox in the samples page fixed diffstat: lib/galaxy/web/controllers/requests_admin.py | 34 ++++++++++++++-------------- templates/admin/requests/show_request.mako | 11 +++++++- templates/requests/show_request.mako | 11 +++++++- 3 files changed, 35 insertions(+), 21 deletions(-) diffs (100 lines): diff -r e3d164679f80 -r e72342f71adc lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Thu May 06 10:08:57 2010 -0400 +++ b/lib/galaxy/web/controllers/requests_admin.py Thu May 06 10:43:13 2010 -0400 @@ -1773,23 +1773,23 @@ message=message, status=status) -# def __sample_datasets(self, trans, **kwd): -# samples = trans.sa_session.query( trans.app.model.Sample ).all() -# for s in samples: -# if s.dataset_files: -# newdf = [] -# for df in s.dataset_files: -# if type(s.dataset_files[0]) == type([1,2]): -# filepath = df[0] -# status = df[1] -# newdf.append(dict(filepath=filepath, -# status=status, -# name=filepath.split('/')[-1], -# error_msg='', -# size='Unknown')) -# s.dataset_files = newdf -# trans.sa_session.add( s ) -# trans.sa_session.flush() + def __sample_datasets(self, trans, **kwd): + samples = trans.sa_session.query( trans.app.model.Sample ).all() + for s in samples: + if s.dataset_files: + newdf = [] + for df in s.dataset_files: + if type(s.dataset_files[0]) == type([1,2]): + filepath = df[0] + status = df[1] + newdf.append(dict(filepath=filepath, + status=status, + name=filepath.split('/')[-1], + error_msg='', + size='Unknown')) + s.dataset_files = newdf + trans.sa_session.add( s ) + trans.sa_session.flush() # ## #### Request Type Stuff ################################################### diff -r e3d164679f80 -r e72342f71adc templates/admin/requests/show_request.mako --- a/templates/admin/requests/show_request.mako Thu May 06 10:08:57 2010 -0400 +++ b/templates/admin/requests/show_request.mako Thu May 06 10:43:13 2010 -0400 @@ -292,6 +292,11 @@ </select> %elif field['type'] == 'WorkflowField': <select name="sample_${index}_field_${field_index}"> + %if str(sample_values[field_index]) == 'none': + <option value="none" selected>Select one</option> + %else: + <option value="none">Select one</option> + %endif %for option_index, option in enumerate(request.user.stored_workflows): %if not option.deleted: %if str(option.id) == str(sample_values[field_index]): @@ -320,8 +325,10 @@ <td> %if sample_values[field_index]: %if field['type'] == 'WorkflowField': - <% workflow = trans.sa_session.query( trans.app.model.StoredWorkflow ).get( int(sample_values[field_index]) ) %> - <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id(workflow.id) )}">${workflow.name}</a> + %if str(sample_values[field_index]) != 'none': + <% workflow = trans.sa_session.query( trans.app.model.StoredWorkflow ).get( int(sample_values[field_index]) ) %> + <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id(workflow.id) )}">${workflow.name}</a> + %endif %else: ${sample_values[field_index]} %endif diff -r e3d164679f80 -r e72342f71adc templates/requests/show_request.mako --- a/templates/requests/show_request.mako Thu May 06 10:08:57 2010 -0400 +++ b/templates/requests/show_request.mako Thu May 06 10:43:13 2010 -0400 @@ -214,6 +214,11 @@ </select> %elif field['type'] == 'WorkflowField': <select name="sample_${index}_field_${field_index}"> + %if str(sample_values[field_index]) == 'none': + <option value="none" selected>Select one</option> + %else: + <option value="none">Select one</option> + %endif %for option_index, option in enumerate(request.user.stored_workflows): %if not option.deleted: %if str(option.id) == str(sample_values[field_index]): @@ -242,8 +247,10 @@ <td> %if sample_values[field_index]: %if field['type'] == 'WorkflowField': - <% workflow = trans.sa_session.query( trans.app.model.StoredWorkflow ).get( int(sample_values[field_index]) ) %> - <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id(workflow.id) )}">${workflow.name}</a> + %if str(sample_values[field_index]) != 'none': + <% workflow = trans.sa_session.query( trans.app.model.StoredWorkflow ).get( int(sample_values[field_index]) ) %> + <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id(workflow.id) )}">${workflow.name}</a> + %endif %else: ${sample_values[field_index]} %endif

1 0

[hg] galaxy 3746: Fix for downloading a library dataset from the...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/e3d164679f80 changeset: 3746:e3d164679f80 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Thu May 06 10:08:57 2010 -0400 description: Fix for downloading a library dataset from the library dataset's info page. diffstat: templates/library/common/ldda_info.mako | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (12 lines): diff -r ab83e2ef8a99 -r e3d164679f80 templates/library/common/ldda_info.mako --- a/templates/library/common/ldda_info.mako Wed May 05 11:34:29 2010 -0400 +++ b/templates/library/common/ldda_info.mako Thu May 06 10:08:57 2010 -0400 @@ -58,7 +58,7 @@ %endif %if cntrller=='library' and ldda.has_data: <a class="action-button" href="${h.url_for( controller='library_common', action='act_on_multiple_datasets', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), ldda_ids=trans.security.encode_id( ldda.id ), do_action='import_to_history', use_panels=use_panels, show_deleted=show_deleted )}">Import this dataset into your current history</a> - <a class="action-button" href="${h.url_for( controller='library', action='download_dataset_from_folder', cntrller=cntrller, id=trans.security.encode_id( ldda.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Download this dataset</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='download_dataset_from_folder', cntrller=cntrller, id=trans.security.encode_id( ldda.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Download this dataset</a> %endif </div> %endif

1 0

[hg] galaxy 3745: Enhanced column join to allow user to specify ...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/ab83e2ef8a99 changeset: 3745:ab83e2ef8a99 user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Wed May 05 11:34:29 2010 -0400 description: Enhanced column join to allow user to specify fill values for empty columns, either one value for all or by column diffstat: test-data/column_join_out1.pileup | 120 +++++++++++++++--------------- test-data/column_join_out2.pileup | 80 ++++++++++---------- test-data/column_join_out3.pileup | 140 +++++++++++++++++----------------- tools/new_operations/column_join.py | 120 +++++++++++++++++++++++------ tools/new_operations/column_join.xml | 86 ++++++++++++++++++--- 5 files changed, 337 insertions(+), 209 deletions(-) diffs (667 lines): diff -r 5f59c890ee8d -r ab83e2ef8a99 test-data/column_join_out1.pileup --- a/test-data/column_join_out1.pileup Tue May 04 22:27:05 2010 -0400 +++ b/test-data/column_join_out1.pileup Wed May 05 11:34:29 2010 -0400 @@ -1,60 +1,60 @@ -chr1 1 T T 87 25 G G 25 25 -chr1 2 A T 87 25 T T 25 25 -chr1 3 A G 87 25 T T 27 25 -chr1 4 A T 55 25 A A 36 25 -chr1 5 C A 54 25 A A 36 25 -chr1 6 G T 87 25 T T 36 25 -chr1 7 A C 87 25 G G 42 25 -chr1 8 G A 87 25 T T 45 25 -chr1 9 A T 87 25 A A 51 25 -chr1 10 G A 57 25 G G 54 25 -chr1 11 C A 57 25 C C 57 25 -chr1 12 T A 99 25 T T 60 25 -chr1 13 A C 99 25 T T 78 25 -chr1 14 G C 55 25 A A 56 25 -chr1 15 T G 68 25 A A 87 25 -chr4 1 T T 90 25 -chr4 2 A A 87 25 -chr4 3 A A 34 25 -chr4 4 T T 55 25 -chr4 5 A A 54 25 -chr4 6 T T 87 25 -chr4 7 A A 80 25 -chr4 8 A A 87 25 -chr4 9 A A 87 25 -chr4 10 G G 57 25 -chr4 11 C C 57 25 -chr4 12 A A 99 25 -chr4 13 A A 99 25 -chr4 14 G G 55 25 -chr4 15 G G 68 25 -chrM 1 A G 25 25 T G 25 25 -chrM 2 C T 25 25 C A 25 25 -chrM 3 T G 27 25 C A 25 25 -chrM 4 G C 36 25 G A 36 25 -chrM 5 T A 38 25 A T 36 25 -chrM 6 T A 39 25 A G 36 25 -chrM 7 G C 43 25 C G 42 25 -chrM 8 A C 46 25 T T 45 25 -chrM 9 T G 53 25 C A 51 25 -chrM 10 T G 56 25 G G 54 25 -chrM 11 C G 57 25 T C 57 25 -chrM 12 T C 61 25 A T 60 25 -chrM 13 T G 79 25 A T 78 25 -chrM 14 A C 58 25 G A 56 25 -chrM 15 G A 87 25 G A 87 25 -chrM 16 G C 88 25 -chrM 17 A C 88 25 -chrM 18 G A 89 25 -chrM 19 G T 58 25 -chrM 20 T C 55 25 -chrM 21 C T 87 25 -chrM 22 C A 87 25 -chrM 23 A G 87 25 -chrM 24 A T 89 25 -chrM 25 G A 57 25 -chrM 26 C G 58 25 -chrM 27 T A 99 25 -chrM 28 A C 99 25 -chrM 29 G C 58 25 -chrM 30 T T 65 25 +chr1 1 ? ? ? ? T T 87 25 G G 25 25 +chr1 2 ? ? ? ? A T 87 25 T T 25 25 +chr1 3 ? ? ? ? A G 87 25 T T 27 25 +chr1 4 ? ? ? ? A T 55 25 A A 36 25 +chr1 5 ? ? ? ? C A 54 25 A A 36 25 +chr1 6 ? ? ? ? G T 87 25 T T 36 25 +chr1 7 ? ? ? ? A C 87 25 G G 42 25 +chr1 8 ? ? ? ? G A 87 25 T T 45 25 +chr1 9 ? ? ? ? A T 87 25 A A 51 25 +chr1 10 ? ? ? ? G A 57 25 G G 54 25 +chr1 11 ? ? ? ? C A 57 25 C C 57 25 +chr1 12 ? ? ? ? T A 99 25 T T 60 25 +chr1 13 ? ? ? ? A C 99 25 T T 78 25 +chr1 14 ? ? ? ? G C 55 25 A A 56 25 +chr1 15 ? ? ? ? T G 68 25 A A 87 25 +chr4 1 ? ? ? ? ? ? ? ? T T 90 25 +chr4 2 ? ? ? ? ? ? ? ? A A 87 25 +chr4 3 ? ? ? ? ? ? ? ? A A 34 25 +chr4 4 ? ? ? ? ? ? ? ? T T 55 25 +chr4 5 ? ? ? ? ? ? ? ? A A 54 25 +chr4 6 ? ? ? ? ? ? ? ? T T 87 25 +chr4 7 ? ? ? ? ? ? ? ? A A 80 25 +chr4 8 ? ? ? ? ? ? ? ? A A 87 25 +chr4 9 ? ? ? ? ? ? ? ? A A 87 25 +chr4 10 ? ? ? ? ? ? ? ? G G 57 25 +chr4 11 ? ? ? ? ? ? ? ? C C 57 25 +chr4 12 ? ? ? ? ? ? ? ? A A 99 25 +chr4 13 ? ? ? ? ? ? ? ? A A 99 25 +chr4 14 ? ? ? ? ? ? ? ? G G 55 25 +chr4 15 ? ? ? ? ? ? ? ? G G 68 25 +chrM 1 A G 25 25 T G 25 25 ? ? ? ? +chrM 2 C T 25 25 C A 25 25 ? ? ? ? +chrM 3 T G 27 25 C A 25 25 ? ? ? ? +chrM 4 G C 36 25 G A 36 25 ? ? ? ? +chrM 5 T A 38 25 A T 36 25 ? ? ? ? +chrM 6 T A 39 25 A G 36 25 ? ? ? ? +chrM 7 G C 43 25 C G 42 25 ? ? ? ? +chrM 8 A C 46 25 T T 45 25 ? ? ? ? +chrM 9 T G 53 25 C A 51 25 ? ? ? ? +chrM 10 T G 56 25 G G 54 25 ? ? ? ? +chrM 11 C G 57 25 T C 57 25 ? ? ? ? +chrM 12 T C 61 25 A T 60 25 ? ? ? ? +chrM 13 T G 79 25 A T 78 25 ? ? ? ? +chrM 14 A C 58 25 G A 56 25 ? ? ? ? +chrM 15 G A 87 25 G A 87 25 ? ? ? ? +chrM 16 G C 88 25 ? ? ? ? ? ? ? ? +chrM 17 A C 88 25 ? ? ? ? ? ? ? ? +chrM 18 G A 89 25 ? ? ? ? ? ? ? ? +chrM 19 G T 58 25 ? ? ? ? ? ? ? ? +chrM 20 T C 55 25 ? ? ? ? ? ? ? ? +chrM 21 C T 87 25 ? ? ? ? ? ? ? ? +chrM 22 C A 87 25 ? ? ? ? ? ? ? ? +chrM 23 A G 87 25 ? ? ? ? ? ? ? ? +chrM 24 A T 89 25 ? ? ? ? ? ? ? ? +chrM 25 G A 57 25 ? ? ? ? ? ? ? ? +chrM 26 C G 58 25 ? ? ? ? ? ? ? ? +chrM 27 T A 99 25 ? ? ? ? ? ? ? ? +chrM 28 A C 99 25 ? ? ? ? ? ? ? ? +chrM 29 G C 58 25 ? ? ? ? ? ? ? ? +chrM 30 T T 65 25 ? ? ? ? ? ? ? ? diff -r 5f59c890ee8d -r ab83e2ef8a99 test-data/column_join_out2.pileup --- a/test-data/column_join_out2.pileup Tue May 04 22:27:05 2010 -0400 +++ b/test-data/column_join_out2.pileup Wed May 05 11:34:29 2010 -0400 @@ -1,15 +1,15 @@ -chr1 1 C 1 -chr1 2 G 2 -chr1 3 A 2 -chr1 4 C 2 -chr1 5 T 3 -chr1 6 G 3 -chr1 7 C 4 -chr1 8 A 4 -chr1 9 T 5 -chr1 10 G 5 -chr1 11 A 5 -chr1 12 C 5 +chr1 1 C 1 +chr1 2 G 2 +chr1 3 A 2 +chr1 4 C 2 +chr1 5 T 3 +chr1 6 G 3 +chr1 7 C 4 +chr1 8 A 4 +chr1 9 T 5 +chr1 10 G 5 +chr1 11 A 5 +chr1 12 C 5 chr1 42 T 1 C 1 chr1 43 G 2 C 2 chr1 44 T 2 T 2 @@ -20,21 +20,21 @@ chr1 49 C 5 G 5 chr1 50 A 5 A 5 chr1 51 A 5 G 5 -chr1 52 A 5 -chr1 53 G 5 -chr2 1 T 6 -chr2 2 G 6 -chr2 3 C 7 -chr2 4 G 7 -chr2 5 G 7 -chr2 6 A 7 -chr2 7 T 8 -chr2 8 A 8 -chr2 9 C 9 -chr2 10 T 9 -chr2 11 C 10 -chr2 12 G 10 -chr2 13 A 11 +chr1 52 A 5 +chr1 53 G 5 +chr2 1 T 6 +chr2 2 G 6 +chr2 3 C 7 +chr2 4 G 7 +chr2 5 G 7 +chr2 6 A 7 +chr2 7 T 8 +chr2 8 A 8 +chr2 9 C 9 +chr2 10 T 9 +chr2 11 C 10 +chr2 12 G 10 +chr2 13 A 11 chr2 52 T 5 chr2 53 A 5 chr2 54 T 5 @@ -43,19 +43,19 @@ chr2 57 T 5 chr2 58 T 6 chr2 59 A 6 -chr2 77 C 6 -chr2 78 G 6 -chr2 79 T 7 -chr2 80 C 7 -chr2 81 G 7 -chr2 82 A 8 -chr2 83 A 8 -chr2 84 T 8 -chr2 85 G 8 -chr2 86 C 9 -chr2 87 G 9 -chr2 88 G 10 -chr2 89 G 10 +chr2 77 C 6 +chr2 78 G 6 +chr2 79 T 7 +chr2 80 C 7 +chr2 81 G 7 +chr2 82 A 8 +chr2 83 A 8 +chr2 84 T 8 +chr2 85 G 8 +chr2 86 C 9 +chr2 87 G 9 +chr2 88 G 10 +chr2 89 G 10 chr3 60 C 6 chr3 61 T 6 chr3 62 C 6 diff -r 5f59c890ee8d -r ab83e2ef8a99 test-data/column_join_out3.pileup --- a/test-data/column_join_out3.pileup Tue May 04 22:27:05 2010 -0400 +++ b/test-data/column_join_out3.pileup Wed May 05 11:34:29 2010 -0400 @@ -1,70 +1,70 @@ -chr1 1 C 1 ^:. -chr1 2 G 2 .^:. -chr1 3 A 2 .. -chr1 4 C 2 .. -chr1 5 T 3 ..^:. -chr1 6 G 3 ..^:, -chr1 7 C 4 .N., -chr1 8 A 4 ..., -chr1 9 T 5 ..C., -chr1 10 G 5 N..., -chr1 11 A 5 .C.., -chr1 12 C 5 ..N., -chr1 42 T 1 ^:. C 1 ^:. -chr1 43 G 2 .^:. C 2 .^:. -chr1 44 T 2 .. T 2 .. -chr1 45 C 3 ..^:. A 3 ..^:. -chr1 46 G 3 ..^:. G 4 ...^:. -chr1 47 T 4 ...^:, A 5 ....^:, -chr1 48 A 4 .N., T 5 ...N, -chr1 49 C 5 ...., G 5 ...., -chr1 50 A 5 ..G., A 5 .G.., -chr1 51 A 5 A..., G 5 ...., -chr1 52 A 5 ...., -chr1 53 G 5 ..N., -chr2 1 T 6 .C..., -chr2 2 G 6 ..N.., -chr2 3 C 7 ..C..., -chr2 4 G 7 .G...., -chr2 5 G 7 ...N.., -chr2 6 A 7 ..T..., -chr2 7 T 8 ...C..., -chr2 8 A 8 ..A...., -chr2 9 C 9 .GA..N.., -chr2 10 T 9 ........, -chr2 11 C 10 .>>..T..., -chr2 12 G 10 .N..G...., -chr2 13 A 11 ....A..T.., -chr2 14 G 11 ..N....... -chr2 15 C 11 A.....NG.. -chr2 16 T 11 ...C.....G -chr2 17 C 12 G......TN.. -chr2 18 A 12 N......G..A -chr2 19 A 13 .......NN... -chr2 20 C 13 ..GT.......N -chr2 52 T 5 .N.., -chr2 53 A 5 ...., -chr2 54 T 5 ...., -chr2 55 T 5 ...., -chr2 56 C 5 ...., -chr2 57 T 5 ...., -chr2 58 T 6 .N..., -chr2 59 A 6 ....., -chr2 77 C 6 .G..., -chr2 78 G 6 ..N.., -chr2 79 T 7 ..N..., -chr2 80 C 7 .G...., -chr2 81 G 7 ...A.., -chr2 82 A 8 ...G..., -chr2 83 A 8 ...T..., -chr2 84 T 8 ..A...., -chr2 85 G 8 .GA...., -chr2 86 C 9 ........, -chr2 87 G 9 ....T..., -chr3 60 C 6 ...G., -chr3 61 T 6 ..N.., -chr3 62 C 6 ...A., -chr3 63 C 7 .N...., -chr3 64 A 7 ...G.., -chr3 65 T 7 ...AA., -chr3 66 A 7 ....N., +chr1 1 C 1 ^:. X X +chr1 2 G 2 .^:. X X +chr1 3 A 2 .. X X +chr1 4 C 2 .. X X +chr1 5 T 3 ..^:. X X +chr1 6 G 3 ..^:, X X +chr1 7 C 4 .N., X X +chr1 8 A 4 ..., X X +chr1 9 T 5 ..C., X X +chr1 10 G 5 N..., X X +chr1 11 A 5 .C.., X X +chr1 12 C 5 ..N., X X +chr1 42 X T 1 ^:. C 1 ^:. +chr1 43 X G 2 .^:. C 2 .^:. +chr1 44 X T 2 .. T 2 .. +chr1 45 X C 3 ..^:. A 3 ..^:. +chr1 46 X G 3 ..^:. G 4 ...^:. +chr1 47 X T 4 ...^:, A 5 ....^:, +chr1 48 X A 4 .N., T 5 ...N, +chr1 49 X C 5 ...., G 5 ...., +chr1 50 X A 5 ..G., A 5 .G.., +chr1 51 X A 5 A..., G 5 ...., +chr1 52 X A 5 ...., X +chr1 53 X G 5 ..N., X +chr2 1 T 6 .C..., X X +chr2 2 G 6 ..N.., X X +chr2 3 C 7 ..C..., X X +chr2 4 G 7 .G...., X X +chr2 5 G 7 ...N.., X X +chr2 6 A 7 ..T..., X X +chr2 7 T 8 ...C..., X X +chr2 8 A 8 ..A...., X X +chr2 9 C 9 .GA..N.., X X +chr2 10 T 9 ........, X X +chr2 11 C 10 .>>..T..., X X +chr2 12 G 10 .N..G...., X X +chr2 13 A 11 ....A..T.., X X +chr2 14 G 11 ..N....... X X +chr2 15 C 11 A.....NG.. X X +chr2 16 T 11 ...C.....G X X +chr2 17 C 12 G......TN.. X X +chr2 18 A 12 N......G..A X X +chr2 19 A 13 .......NN... X X +chr2 20 C 13 ..GT.......N X X +chr2 52 X X T 5 .N.., +chr2 53 X X A 5 ...., +chr2 54 X X T 5 ...., +chr2 55 X X T 5 ...., +chr2 56 X X C 5 ...., +chr2 57 X X T 5 ...., +chr2 58 X X T 6 .N..., +chr2 59 X X A 6 ....., +chr2 77 X C 6 .G..., X +chr2 78 X G 6 ..N.., X +chr2 79 X T 7 ..N..., X +chr2 80 X C 7 .G...., X +chr2 81 X G 7 ...A.., X +chr2 82 X A 8 ...G..., X +chr2 83 X A 8 ...T..., X +chr2 84 X T 8 ..A...., X +chr2 85 X G 8 .GA...., X +chr2 86 X C 9 ........, X +chr2 87 X G 9 ....T..., X +chr3 60 X X C 6 ...G., +chr3 61 X X T 6 ..N.., +chr3 62 X X C 6 ...A., +chr3 63 X X C 7 .N...., +chr3 64 X X A 7 ...G.., +chr3 65 X X T 7 ...AA., +chr3 66 X X A 7 ....N., diff -r 5f59c890ee8d -r ab83e2ef8a99 tools/new_operations/column_join.py --- a/tools/new_operations/column_join.py Tue May 04 22:27:05 2010 -0400 +++ b/tools/new_operations/column_join.py Wed May 05 11:34:29 2010 -0400 @@ -13,7 +13,19 @@ """ -import os, re, sys, tempfile +import optparse, os, re, struct, sys, tempfile + +try: + simple_json_exception = None + from galaxy import eggs + from galaxy.util.bunch import Bunch + from galaxy.util import stringify_dictionary_keys + import pkg_resources + pkg_resources.require("simplejson") + import simplejson +except Exception, e: + simplejson_exception = e + simplejson = None def stop_err( msg ): sys.stderr.write( msg ) @@ -136,17 +148,50 @@ return '%s\t%s' % tuple( min_ref_pos ), min_loc def __main__(): - output = sys.argv[1] - input1 = sys.argv[2] - input2 = sys.argv[3] - hinge = int( sys.argv[4] ) - cols = [ int( c ) for c in sys.argv[5].split( ',' ) ] - inputs = sys.argv[6:] - assert len( cols ) > 2, 'You need to select at least one column in addition to the first two' + parser = optparse.OptionParser() + parser.add_option( '', '--output', dest='output', help='' ) + parser.add_option( '', '--input1', dest='input1', help='' ) + parser.add_option( '', '--input2', dest='input2', help='' ) + parser.add_option( '', '--hinge', dest='hinge', help='' ) + parser.add_option( '', '--columns', dest='columns', help='' ) + parser.add_option( '', '--fill_options_file', dest='fill_options_file', default=None, help='' ) + (options, args) = parser.parse_args() + output = options.output + input1 = options.input1 + input2 = options.input2 + hinge = int( options.hinge ) + cols = [ int( c ) for c in str( options.columns ).split( ',' ) if int( c ) > hinge ] + inputs = [ input1, input2 ] + if options.fill_options_file == "None": + inputs.extend( args ) + else: + try: + col = int( args[0] ) + except ValueError: + inputs.extend( args ) + fill_options = None + if options.fill_options_file != "None" and options.fill_options_file is not None: + try: + if simplejson is None: + raise simplejson_exception + fill_options = Bunch( **stringify_dictionary_keys( simplejson.load( open( options.fill_options_file ) ) ) ) + except Exception, e: + print "Warning: Ignoring fill options due to simplejson error (%s)." % e + if fill_options is None: + fill_options = Bunch() + if 'file1_columns' not in fill_options: + fill_options.file1_columns = None + if fill_options and fill_options.file1_columns: + fill_empty = {} + for col in cols: + fill_empty[ col ] = fill_options.file1_columns[ col - 1 ] + else: + fill_empty = None + assert len( cols ) > 0, 'You need to select at least one column in addition to the hinge' + delimiter = '\t' # make sure all files are sorted in same way, ascending tmp_input_files = [] - input_files = [ input1, input2 ] - input_files.extend( inputs ) + input_files = inputs[:] for in_file in input_files: tmp_file = tempfile.NamedTemporaryFile() tmp_file_name = tmp_file.name @@ -162,10 +207,9 @@ current_lines = [ f.readline() for f in tmp_input_files ] last_lines = ''.join( current_lines ).strip() last_loc = -1 - i = 0 while last_lines: # get the "minimum" hinge, which should come first, and the file location in list - hinges = [ '\t'.join( line.split( '\t' )[ :hinge ] ) for line in current_lines ] + hinges = [ delimiter.join( line.split( delimiter )[ :hinge ] ) for line in current_lines ] hinge_dict = {} for i in range( len( hinges ) ): if not hinge_dict.has_key( hinges[ i ] ): @@ -174,33 +218,59 @@ hinges = [ h for h in hinges if h ] current, loc = hinges[0], hinge_dict[ hinges[0] ] # first output empty columns for vertical alignment (account for "missing" files) + # write output if trailing empty columns + current_data = [] if current != old_current: - last_loc = -1 - if loc - last_loc > 1: - current_data = [ '' for col in range( ( loc - last_loc - 1 ) * len( [ col for col in cols if col > hinge ] ) ) ] + # fill trailing empty columns with appropriate fill value + if not first_line: + if last_loc < len( inputs ) - 1: + if not fill_empty: + filler = [ '' for col in range( ( len( inputs ) - last_loc - 1 ) * len( cols ) ) ] + else: + filler = [ fill_empty[ cols[ col % len( cols ) ] ] for col in range( ( len( inputs ) - last_loc - 1 ) * len( cols ) ) ] + fout.write( '%s%s' % ( delimiter, delimiter.join( filler ) ) ) + # insert line break before current line + fout.write( '\n' ) + # fill leading empty columns with appropriate fill value + if loc > 0: + if not fill_empty: + current_data = [ '' for col in range( loc * len( cols ) ) ] + else: + current_data = [ fill_empty[ cols[ col % len( cols ) ] ] for col in range( loc * len( cols ) ) ] else: - current_data = [] + if loc - last_loc > 1: + if not fill_empty: + current_data = [ '' for col in range( ( loc - last_loc - 1 ) * len( cols ) ) ] + else: + current_data = [ fill_empty[ cols[ col % len( cols ) ] ] for col in range( ( loc - last_loc - 1 ) * len( cols ) ) ] # now output actual data - split_line = current_lines[ loc ].strip().split( '\t' ) + split_line = current_lines[ loc ].strip().split( delimiter ) if ''.join( split_line ): + # add actual data to be output below for col in cols: if col > hinge: current_data.append( split_line[ col - 1 ] ) + # grab next line for selected file current_lines[ loc ] = tmp_input_files[ loc ].readline() + # write relevant data to file if current == old_current: - if current_data: - fout.write( '\t%s' % '\t'.join( current_data ) ) + fout.write( '%s%s' % ( delimiter, delimiter.join( current_data ) ) ) else: - if not first_line: - fout.write( '\n' ) - fout.write( '%s\t%s' % ( current, '\t'.join( current_data ) ) ) - first_line = False + fout.write( '%s%s%s' % ( current, delimiter, delimiter.join( current_data ) ) ) + last_loc = loc old_current = current last_lines = ''.join( current_lines ).strip() - last_loc = loc + first_line = False + # fill trailing empty columns for final line + if last_loc < len( inputs ) - 1: + if not fill_empty: + filler = [ '' for col in range( ( len( inputs ) - last_loc - 1 ) * len( cols ) ) ] + else: + filler = [ fill_empty[ cols[ col % len( cols ) ] ] for col in range( ( len( inputs ) - last_loc - 1 ) * len( cols ) ) ] + fout.write( '%s%s' % ( delimiter, delimiter.join( filler ) ) ) fout.write( '\n' ) + fout.close() for f in tmp_input_files: os.unlink( f.name ) - fout.close() if __name__ == "__main__" : __main__() diff -r 5f59c890ee8d -r ab83e2ef8a99 tools/new_operations/column_join.xml --- a/tools/new_operations/column_join.xml Tue May 04 22:27:05 2010 -0400 +++ b/tools/new_operations/column_join.xml Wed May 05 11:34:29 2010 -0400 @@ -2,53 +2,111 @@ <description></description> <command interpreter="python"> column_join.py - $output - $input1 - $input2 - $hinge - $columns + --output=$output + --input1=$input1 + --input2=$input2 + --hinge=$hinge + --columns=$columns + #if $fill_empty_columns.fill_empty_columns_switch == "fill_empty": + --fill_options_file=$fill_options_file + #end if #for $f in $file_chooser: ${f.input} #end for </command> <inputs> <param name="input1" type="data" format="tabular" label="Choose the first file for the join" /> + <param name="hinge" type="data_column" data_ref="input1" multiple="false" numerical="false" label="Use this column and columns to left the 'hinge' (matching data for each join)" help="All columns to left of selected column (plus selected column) will be used. Select 2 for pileup" /> <param name="columns" type="data_column" data_ref="input1" multiple="true" numerical="false" label="Include these column" help="Multi-select list - hold the appropriate key while clicking to select multiple columns" /> - <param name="hinge" type="data_column" data_ref="input1" multiple="false" numerical="false" label="Use this column and columns to left the 'hinge' (matching data for each join)" help="All columns to left of selected column (plus selected column) will be used. Select 2 for pileup" /> + <conditional name="fill_empty_columns"> + <param name="fill_empty_columns_switch" type="select" label="Fill empty columns"> + <option value="no_fill" selected="True">No</option> + <option value="fill_empty">Yes</option> + </param> + <when value="no_fill" /> + <when value="fill_empty"> + <conditional name="do_fill_empty_columns"> + <param name="column_fill_type" type="select" label="Fill Columns by"> + <option value="single_fill_value" selected="True">Single fill value</option> + <option value="fill_value_by_column">Values by column</option> + </param> + <when value="single_fill_value"> + <param type="text" name="fill_value" label="Fill value" value="." /> + </when> + <when value="fill_value_by_column"> + <repeat name="column_fill" title="Fill Column"> + <param name="column_number" label="Column" type="data_column" data_ref="input1" /> + <param type="text" name="fill_value" value="." /> + </repeat> + </when> + </conditional> + </when> + </conditional> <param name="input2" type="data" format="tabular" label="Choose the second file for the join" /> <repeat name="file_chooser" title="Additional Input"> <param name="input" label="Additional input file" type="data" format="tabular" /> </repeat> </inputs> + <configfiles> + <configfile name="fill_options_file"><% +import simplejson +%> +#set $__fill_options = {} +#if $fill_empty_columns['fill_empty_columns_switch'] == 'fill_empty': + #if $fill_empty_columns['do_fill_empty_columns']['column_fill_type'] == 'single_fill_value': + #set $__start_fill = $fill_empty_columns['do_fill_empty_columns']['fill_value'].value + #else: + #set $__start_fill = "" + #end if + #set $__fill_options['file1_columns'] = [ __start_fill for i in range( int( $input1.metadata.columns ) ) ] + #if $fill_empty_columns['do_fill_empty_columns']['column_fill_type'] == 'fill_value_by_column': + #for column_fill in $fill_empty_columns['do_fill_empty_columns']['column_fill']: + #set $__fill_options['file1_columns'][ int( column_fill['column_number'].value ) - 1 ] = column_fill['fill_value'].value + #end for + #end if +#end if +${simplejson.dumps( __fill_options )} + </configfile> + </configfiles> <outputs> <data name="output" format="tabular" /> </outputs> <tests> <test> <param name="input1" value="column_join_in1.pileup" ftype="pileup" /> + <param name="hinge" value="2" /> <param name="columns" value="1,2,3,4,5,7" /> - <param name="hinge" value="1,2" /> + <param name="fill_empty_columns_switch" value="fill_empty" /> + <param name="column_fill_type" value="single_fill_value" /> + <param name="fill_value" value="?" /> <param name="input2" value="column_join_in2.pileup" ftype="pileup" /> <param name="input" value="column_join_in3.pileup" ftype="pileup" /> <output name="output" file="column_join_out1.pileup" ftype="tabular" /> </test> <test> <param name="input1" value="column_join_in4.pileup" ftype="pileup" /> + <param name="hinge" value="2" /> <param name="columns" value="1,2,3,4" /> - <param name="hinge" value="1,2" /> + <param name="fill_empty_columns_switch" value="no_fill" /> <param name="input2" value="column_join_in5.pileup" ftype="pileup" /> <param name="input" value="column_join_in6.pileup" ftype="pileup" /> <output name="output" file="column_join_out2.pileup" ftype="tabular" /> </test> + </tests> <help> **What it does**

1 0