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commit/galaxy-central: natefoo: Another bugfix for egg conflicts, don't add items to the pkg_resources working set unless the item's not already in there.
by Bitbucket 10 Feb '11

10 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/6d5331f3b468/ changeset: r5041:6d5331f3b468 user: natefoo date: 2011-02-10 21:53:06 summary: Another bugfix for egg conflicts, don't add items to the pkg_resources working set unless the item's not already in there. affected #: 1 file (79 bytes) --- a/lib/galaxy/eggs/__init__.py Thu Feb 10 15:29:08 2011 -0500 +++ b/lib/galaxy/eggs/__init__.py Thu Feb 10 15:53:06 2011 -0500 @@ -212,7 +212,8 @@ try: dists = self.resolve() for dist in dists: - pkg_resources.working_set.add( dist ) + if dist.location not in pkg_resources.working_set.entries: + pkg_resources.working_set.add( dist ) return dists except: raise Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Migration script to add a subindex column to the run table.
by Bitbucket 10 Feb '11

10 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/b8442c5e90c9/ changeset: r5040:b8442c5e90c9 user: greg date: 2011-02-10 21:29:08 summary: Migration script to add a subindex column to the run table. affected #: 3 files (108 bytes) --- a/lib/galaxy/model/__init__.py Thu Feb 10 13:58:48 2011 -0500 +++ b/lib/galaxy/model/__init__.py Thu Feb 10 15:29:08 2011 -0500 @@ -2050,9 +2050,10 @@ self.external_service = external_service class Run( object ): - def __init__( self, form_definition, form_values ): + def __init__( self, form_definition, form_values, subindex=None ): self.template = form_definition self.info = form_values + self.subindex = subindex class RequestTypeRunAssociation( object ): def __init__( self, request_type, run ): --- a/lib/galaxy/model/mapping.py Thu Feb 10 13:58:48 2011 -0500 +++ b/lib/galaxy/model/mapping.py Thu Feb 10 15:29:08 2011 -0500 @@ -705,7 +705,8 @@ Column( "update_time", DateTime, default=now, onupdate=now ), Column( "form_definition_id", Integer, ForeignKey( "form_definition.id" ), index=True ), Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ), - Column( "deleted", Boolean, index=True, default=False ) ) + Column( "deleted", Boolean, index=True, default=False ), + Column( "subindex", TrimmedString( 255 ), index=True ) ) RequestTypeRunAssociation.table = Table( "request_type_run_association", metadata, Column( "id", Integer, primary_key=True ), Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: workflows: jquery1.5 fix, quotations.
by Bitbucket 10 Feb '11

10 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/9b43e6baee92/ changeset: r5039:9b43e6baee92 user: dannon date: 2011-02-10 19:58:48 summary: workflows: jquery1.5 fix, quotations. affected #: 2 files (4 bytes) --- a/static/scripts/galaxy.workflow_editor.canvas.js Thu Feb 10 12:13:55 2011 -0500 +++ b/static/scripts/galaxy.workflow_editor.canvas.js Thu Feb 10 13:58:48 2011 -0500 @@ -409,7 +409,7 @@ var t = $("<div class='terminal input-terminal'></div>"); node.enable_input_terminal( t, input.name, input.extensions ); // If already connected save old connection - old_body.find( "div[name=" + input.name + "]" ).each( function() { + old_body.find( "div[name='" + input.name + "']" ).each( function() { $(this).find( ".input-terminal" ).each( function() { var c = this.terminal.connectors[0]; if ( c ) { --- a/static/scripts/packed/galaxy.workflow_editor.canvas.js Thu Feb 10 12:13:55 2011 -0500 +++ b/static/scripts/packed/galaxy.workflow_editor.canvas.js Thu Feb 10 13:58:48 2011 -0500 @@ -1,1 +1,1 @@ -function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}OutputTerminal.prototype=new Terminal();function InputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1){for(var c in this.datatypes){var f=new Array();f=f.concat(a.datatypes);if(a.node.post_job_actions){for(var d in a.node.post_job_actions){var g=a.node.post_job_actions[d];if(g.action_type=="ChangeDatatypeAction"&&(g.output_name==""||g.output_name==a.name)&&g.action_arguments){f.push(g.action_arguments.newtype)}}}for(var b in f){if(f[b]=="input"||issubtype(f[b],this.datatypes[c])){return true}}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a){this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;this.handle1.connect(this);this.handle2=a;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*f;this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(d,a,b){var c=this;$(d).each(function(){var f=this.terminal=new InputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dropinit",function(g,h){return $(h.drag).hasClass("output-terminal")&&f.can_accept(h.drag.terminal)}).bind("dropstart",function(g,h){h.proxy.terminal.connectors[0].inner_color="#BBFFBB"}).bind("dropend",function(g,h){h.proxy.terminal.connectors[0].inner_color="#FFFFFF"}).bind("drop",function(g,h){(new Connector(h.drag.terminal,f)).redraw()}).bind("hover",function(){if(f.connectors.length>0){var g=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img/>").attr("src",image_path+"/delete_icon.png").click(function(){$.each(f.connectors,function(i,h){h.destroy()});g.remove()}))).bind("mouseleave",function(){$(this).remove()});g.css({top:$(this).offset().top-2,left:$(this).offset().left-g.width(),"padding-right":$(this).width()}).show()}});c.input_terminals[a]=f})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j,k){$(k.available).addClass("input-terminal-active");workflow.check_changes_in_active_form();var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var l=new Connector();l.dragging=true;l.connect(this.terminal,i.terminal);return i}).bind("drag",function(i,j){var h=function(){var l=$(j.proxy).offsetParent().offset(),k=j.offsetX-l.left,m=j.offsetY-l.top;$(j.proxy).css({left:k,top:m});j.proxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h,i){i.proxy.terminal.connectors[0].destroy();$(i.proxy).remove();$(i.available).removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b.appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(h){var g=this.element;if(h.type){this.type=h.type}this.name=h.name;this.form_html=h.form_html;this.tool_state=h.tool_state;this.tool_errors=h.tool_errors;this.tooltip=h.tooltip?h.tooltip:"";this.annotation=h.annotation;this.post_job_actions=h.post_job_actions?h.post_job_actions:{};this.workflow_outputs=h.workflow_outputs?h.workflow_outputs:[];if(this.tool_errors){g.addClass("tool-node-error")}else{g.removeClass("tool-node-error")}var d=this;var c=Math.max(150,g.width());var a=g.find(".toolFormBody");a.find("div").remove();var i=$("<div class='inputs'></div>").appendTo(a);$.each(h.data_inputs,function(k,f){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,f.name,f.extensions);var b=$("<div class='form-row dataRow input-data-row' name='"+f.name+"'>"+f.label+"</div>");b.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(b);c=Math.max(c,b.outerWidth());b.css({position:"",left:"",top:"",display:""});b.remove();i.append(b.prepend(j))});if((h.data_inputs.length>0)&&(h.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(h.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");d.enable_output_terminal(j,b.name,b.extensions);var f=b.name;if(b.extensions.indexOf("input")<0){f=f+" ("+b.extensions.join(", ")+")"}var m=$("<div class='form-row dataRow'>"+f+"</div>");if(d.type=="tool"){var l=$("<div class='callout'></div>").css({display:"none"}).append($("<div class='buttons'></div>").append($("<img/>").attr("src",image_path+"/fugue/asterisk-small-outline.png").click(function(){if($.inArray(b.name,d.workflow_outputs)!=-1){d.workflow_outputs.splice($.inArray(b.name,d.workflow_outputs),1);l.find("img").attr("src",image_path+"/fugue/asterisk-small-outline.png")}else{d.workflow_outputs.push(b.name);l.find("img").attr("src",image_path+"/fugue/asterisk-small.png")}workflow.has_changes=true;canvas_manager.draw_overview()}))).tipsy({delayIn:500,fallback:"Flag this as a workflow output. All non-flagged outputs will be hidden."});l.css({top:"50%",margin:"-8px 0px 0px 0px",right:8});l.show();m.append(l);if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",image_path+"/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",image_path+"/fugue/asterisk-small.png")}m.hover(function(){l.find("img").attr("src",image_path+"/fugue/asterisk-small-yellow.png")},function(){if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",image_path+"/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",image_path+"/fugue/asterisk-small.png")}})}m.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(m);c=Math.max(c,m.outerWidth()+17);m.css({position:"",left:"",top:"",display:""});m.detach();a.append(m.append(j))});g.css("width",Math.min(250,Math.max(g.width(),c)));workflow.node_changed(this)},update_field_data:function(f){var c=$(this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;this.annotation=f.annotation;var g=$.parseJSON(f.post_job_actions);this.post_job_actions=g?g:{};if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var h=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=h.find("div.input-data-row");$.each(f.data_inputs,function(l,j){var k=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(k,j.name,j.extensions);h.find("div[name="+j.name+"]").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){k[0].terminal.connectors[0]=i;i.handle2=k[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+j.name+"'>"+j.label+"</div>").prepend(k))});h.replaceWith(b);h.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_form_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},rectify_workflow_outputs:function(){var a=false;$.each(this.nodes,function(b,c){if(c.workflow_outputs&&c.workflow_outputs.length>0){a=true}});if(a==false){return true}wf=this;$.each(this.nodes,function(b,f){if(f.type=="tool"){var d=false;if(f.post_job_actions==null){f.post_job_actions={}}var c=[];$.each(f.post_job_actions,function(h,g){if(g.action_type=="HideDatasetAction"){c.push(h)}});if(c.length>0&&f==workflow.active_node){$.each(c,function(g,h){d=true;delete f.post_job_actions[h]})}$.each(f.output_terminals,function(h,i){var g=true;$.each(f.workflow_outputs,function(k,l){if(i.name==l){g=false}});if(g==true){d=true;var j={action_type:"HideDatasetAction",output_name:i.name,action_arguments:{}};f.post_job_actions["HideDatasetAction"+i.name]=null;f.post_job_actions["HideDatasetAction"+i.name]=j}});if(wf.active_node==f&&d==true){wf.reload_active_node()}}})},to_simple:function(){var a={};$.each(this.nodes,function(c,f){var g={};$.each(f.input_terminals,function(h,i){g[i.name]=null;$.each(i.connectors,function(j,k){g[i.name]={id:k.handle1.node.id,output_name:k.handle1.name}})});var b={};if(f.post_job_actions){$.each(f.post_job_actions,function(j,h){var k={action_type:h.action_type,output_name:h.output_name,action_arguments:h.action_arguments};b[h.action_type+h.output_name]=null;b[h.action_type+h.output_name]=k})}if(!f.workflow_outputs){f.workflow_outputs=[]}var d={id:f.id,type:f.type,tool_id:f.tool_id,tool_state:f.tool_state,tool_errors:f.tool_errors,input_connections:g,position:$(f.element).position(),annotation:f.annotation,post_job_actions:f.post_job_actions,workflow_outputs:f.workflow_outputs};a[f.id]=d});return{steps:a}},from_simple:function(a){wf=this;var b=0;wf.name=a.name;$.each(a.steps,function(f,d){var c=prebuild_node("tool",d.name,d.tool_id);c.init_field_data(d);if(d.position){c.element.css({top:d.position.top,left:d.position.left})}c.id=d.id;wf.nodes[c.id]=c;b=Math.max(b,parseInt(f))});wf.id_counter=b+1;$.each(a.steps,function(f,d){var c=wf.nodes[f];$.each(d.input_connections,function(h,g){if(g){var i=wf.nodes[g.id];var j=new Connector();j.connect(i.output_terminals[g.output_name],c.input_terminals[h]);j.redraw()}})})},check_changes_in_active_form:function(){if(this.active_form_has_changes){this.has_changes=true;$("#right-content").find("form").submit();this.active_form_has_changes=false}},reload_active_node:function(){if(this.active_node){var a=this.active_node;this.clear_active_node();this.activate_node(a)}},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.check_changes_in_active_form();this.clear_active_node();parent.show_form_for_tool(a.form_html+a.tooltip,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){this.check_changes_in_active_form();parent.show_form_for_tool(a.form_html+a.tooltip,a)}},layout:function(){this.check_changes_in_active_form();this.has_changes=true;var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$(this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></div>");var h="<div><img height='16' align='middle' src='"+image_path+"/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<img/>").attr("src",image_path+"/delete_icon.png").click(function(b){g.destroy()}).hover(function(){$(this).attr("src",image_path+"/delete_icon_dark.png")},function(){$(this).attr("src",image_path+"/delete_icon.png")}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o,p){var f=$(this).offsetParent().offset(),b=p.offsetX-f.left,s=p.offsetY-f.top;$(this).css({left:b,top:s});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.css("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this;var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(){var g=$(this).offset();var f=b.cc.position();c=f.top-g.top;d=f.left-g.left}).bind("drag",function(f,g){a(g.offsetX+d,g.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k,l){var h=b.cc.width(),n=b.cc.height(),m=b.oc.width(),j=b.oc.height(),f=$(this).offsetParent().offset(),i=l.offsetX-f.left,g=l.offsetY-f.top;a(-(i/m*h),-(g/j*n))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g,i){var j=$(this).offsetParent();var h=j.offset();var f=Math.max(j.width()-(i.offsetX-h.left),j.height()-(i.offsetY-h.top));$(this).css({width:f,height:f});b.draw_overview()});$("#overview-border div").bind("drag",function(){})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);$.each(workflow.nodes,function(t,q){i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;if(q.tool_errors){i.fillStyle="#FFCCCC";i.strokeStyle="#AA6666"}else{if(q.workflow_outputs!=undefined&&q.workflow_outputs.length>0){i.fillStyle="#E8A92D";i.strokeStyle="#E8A92D"}}i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}}); \ No newline at end of file +function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}OutputTerminal.prototype=new Terminal();function InputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1){for(var c in this.datatypes){var f=new Array();f=f.concat(a.datatypes);if(a.node.post_job_actions){for(var d in a.node.post_job_actions){var g=a.node.post_job_actions[d];if(g.action_type=="ChangeDatatypeAction"&&(g.output_name==""||g.output_name==a.name)&&g.action_arguments){f.push(g.action_arguments.newtype)}}}for(var b in f){if(f[b]=="input"||issubtype(f[b],this.datatypes[c])){return true}}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a){this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;this.handle1.connect(this);this.handle2=a;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*f;this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(d,a,b){var c=this;$(d).each(function(){var f=this.terminal=new InputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dropinit",function(g,h){return $(h.drag).hasClass("output-terminal")&&f.can_accept(h.drag.terminal)}).bind("dropstart",function(g,h){h.proxy.terminal.connectors[0].inner_color="#BBFFBB"}).bind("dropend",function(g,h){h.proxy.terminal.connectors[0].inner_color="#FFFFFF"}).bind("drop",function(g,h){(new Connector(h.drag.terminal,f)).redraw()}).bind("hover",function(){if(f.connectors.length>0){var g=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img/>").attr("src",image_path+"/delete_icon.png").click(function(){$.each(f.connectors,function(i,h){h.destroy()});g.remove()}))).bind("mouseleave",function(){$(this).remove()});g.css({top:$(this).offset().top-2,left:$(this).offset().left-g.width(),"padding-right":$(this).width()}).show()}});c.input_terminals[a]=f})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j,k){$(k.available).addClass("input-terminal-active");workflow.check_changes_in_active_form();var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var l=new Connector();l.dragging=true;l.connect(this.terminal,i.terminal);return i}).bind("drag",function(i,j){var h=function(){var l=$(j.proxy).offsetParent().offset(),k=j.offsetX-l.left,m=j.offsetY-l.top;$(j.proxy).css({left:k,top:m});j.proxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h,i){i.proxy.terminal.connectors[0].destroy();$(i.proxy).remove();$(i.available).removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b.appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(h){var g=this.element;if(h.type){this.type=h.type}this.name=h.name;this.form_html=h.form_html;this.tool_state=h.tool_state;this.tool_errors=h.tool_errors;this.tooltip=h.tooltip?h.tooltip:"";this.annotation=h.annotation;this.post_job_actions=h.post_job_actions?h.post_job_actions:{};this.workflow_outputs=h.workflow_outputs?h.workflow_outputs:[];if(this.tool_errors){g.addClass("tool-node-error")}else{g.removeClass("tool-node-error")}var d=this;var c=Math.max(150,g.width());var a=g.find(".toolFormBody");a.find("div").remove();var i=$("<div class='inputs'></div>").appendTo(a);$.each(h.data_inputs,function(k,f){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,f.name,f.extensions);var b=$("<div class='form-row dataRow input-data-row' name='"+f.name+"'>"+f.label+"</div>");b.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(b);c=Math.max(c,b.outerWidth());b.css({position:"",left:"",top:"",display:""});b.remove();i.append(b.prepend(j))});if((h.data_inputs.length>0)&&(h.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(h.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");d.enable_output_terminal(j,b.name,b.extensions);var f=b.name;if(b.extensions.indexOf("input")<0){f=f+" ("+b.extensions.join(", ")+")"}var m=$("<div class='form-row dataRow'>"+f+"</div>");if(d.type=="tool"){var l=$("<div class='callout'></div>").css({display:"none"}).append($("<div class='buttons'></div>").append($("<img/>").attr("src",image_path+"/fugue/asterisk-small-outline.png").click(function(){if($.inArray(b.name,d.workflow_outputs)!=-1){d.workflow_outputs.splice($.inArray(b.name,d.workflow_outputs),1);l.find("img").attr("src",image_path+"/fugue/asterisk-small-outline.png")}else{d.workflow_outputs.push(b.name);l.find("img").attr("src",image_path+"/fugue/asterisk-small.png")}workflow.has_changes=true;canvas_manager.draw_overview()}))).tipsy({delayIn:500,fallback:"Flag this as a workflow output. All non-flagged outputs will be hidden."});l.css({top:"50%",margin:"-8px 0px 0px 0px",right:8});l.show();m.append(l);if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",image_path+"/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",image_path+"/fugue/asterisk-small.png")}m.hover(function(){l.find("img").attr("src",image_path+"/fugue/asterisk-small-yellow.png")},function(){if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",image_path+"/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",image_path+"/fugue/asterisk-small.png")}})}m.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(m);c=Math.max(c,m.outerWidth()+17);m.css({position:"",left:"",top:"",display:""});m.detach();a.append(m.append(j))});g.css("width",Math.min(250,Math.max(g.width(),c)));workflow.node_changed(this)},update_field_data:function(f){var c=$(this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;this.annotation=f.annotation;var g=$.parseJSON(f.post_job_actions);this.post_job_actions=g?g:{};if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var h=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=h.find("div.input-data-row");$.each(f.data_inputs,function(l,j){var k=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(k,j.name,j.extensions);h.find("div[name='"+j.name+"']").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){k[0].terminal.connectors[0]=i;i.handle2=k[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+j.name+"'>"+j.label+"</div>").prepend(k))});h.replaceWith(b);h.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_form_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},rectify_workflow_outputs:function(){var a=false;$.each(this.nodes,function(b,c){if(c.workflow_outputs&&c.workflow_outputs.length>0){a=true}});if(a==false){return true}wf=this;$.each(this.nodes,function(b,f){if(f.type=="tool"){var d=false;if(f.post_job_actions==null){f.post_job_actions={}}var c=[];$.each(f.post_job_actions,function(h,g){if(g.action_type=="HideDatasetAction"){c.push(h)}});if(c.length>0&&f==workflow.active_node){$.each(c,function(g,h){d=true;delete f.post_job_actions[h]})}$.each(f.output_terminals,function(h,i){var g=true;$.each(f.workflow_outputs,function(k,l){if(i.name==l){g=false}});if(g==true){d=true;var j={action_type:"HideDatasetAction",output_name:i.name,action_arguments:{}};f.post_job_actions["HideDatasetAction"+i.name]=null;f.post_job_actions["HideDatasetAction"+i.name]=j}});if(wf.active_node==f&&d==true){wf.reload_active_node()}}})},to_simple:function(){var a={};$.each(this.nodes,function(c,f){var g={};$.each(f.input_terminals,function(h,i){g[i.name]=null;$.each(i.connectors,function(j,k){g[i.name]={id:k.handle1.node.id,output_name:k.handle1.name}})});var b={};if(f.post_job_actions){$.each(f.post_job_actions,function(j,h){var k={action_type:h.action_type,output_name:h.output_name,action_arguments:h.action_arguments};b[h.action_type+h.output_name]=null;b[h.action_type+h.output_name]=k})}if(!f.workflow_outputs){f.workflow_outputs=[]}var d={id:f.id,type:f.type,tool_id:f.tool_id,tool_state:f.tool_state,tool_errors:f.tool_errors,input_connections:g,position:$(f.element).position(),annotation:f.annotation,post_job_actions:f.post_job_actions,workflow_outputs:f.workflow_outputs};a[f.id]=d});return{steps:a}},from_simple:function(a){wf=this;var b=0;wf.name=a.name;$.each(a.steps,function(f,d){var c=prebuild_node("tool",d.name,d.tool_id);c.init_field_data(d);if(d.position){c.element.css({top:d.position.top,left:d.position.left})}c.id=d.id;wf.nodes[c.id]=c;b=Math.max(b,parseInt(f))});wf.id_counter=b+1;$.each(a.steps,function(f,d){var c=wf.nodes[f];$.each(d.input_connections,function(h,g){if(g){var i=wf.nodes[g.id];var j=new Connector();j.connect(i.output_terminals[g.output_name],c.input_terminals[h]);j.redraw()}})})},check_changes_in_active_form:function(){if(this.active_form_has_changes){this.has_changes=true;$("#right-content").find("form").submit();this.active_form_has_changes=false}},reload_active_node:function(){if(this.active_node){var a=this.active_node;this.clear_active_node();this.activate_node(a)}},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.check_changes_in_active_form();this.clear_active_node();parent.show_form_for_tool(a.form_html+a.tooltip,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){this.check_changes_in_active_form();parent.show_form_for_tool(a.form_html+a.tooltip,a)}},layout:function(){this.check_changes_in_active_form();this.has_changes=true;var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var 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You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Fix for pysam egg conditional, which would always fail, and actually check always_conditional eggs in the crate's all_eggs method. Fixes downloading of eggs for offline systems.
by Bitbucket 10 Feb '11

10 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/559a9ad2844d/ changeset: r5038:559a9ad2844d user: natefoo date: 2011-02-10 18:13:55 summary: Fix for pysam egg conditional, which would always fail, and actually check always_conditional eggs in the crate's all_eggs method. Fixes downloading of eggs for offline systems. affected #: 1 file (82 bytes) --- a/lib/galaxy/eggs/__init__.py Thu Feb 10 10:33:08 2011 -0500 +++ b/lib/galaxy/eggs/__init__.py Thu Feb 10 12:13:55 2011 -0500 @@ -295,8 +295,9 @@ """ rval = [] for egg in self.eggs.values(): - if egg.name not in self.galaxy_config.always_conditional: - rval.append( egg ) + if egg.name in self.galaxy_config.always_conditional and not self.galaxy_config.check_conditional( egg.name ): + continue + rval.append( egg ) return rval def __getitem__( self, name ): """ @@ -357,7 +358,7 @@ "python_daemon": lambda: sys.version_info[:2] >= ( 2, 5 ), "GeneTrack": lambda: sys.version_info[:2] >= ( 2, 5 ), "ctypes": lambda: ( "drmaa" in self.config.get( "app:main", "start_job_runners" ).split(",") ) and sys.version_info[:2] == ( 2, 4 ), - "pysam": check_pysam() + "pysam": lambda: check_pysam() }.get( egg_name, lambda: True )() except: return False Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guru: Better handling of complex interrupted microsatellites in 'Extract orthologous microsatellites for multiple species alignments' tool.
by Bitbucket 10 Feb '11

10 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/d5ce1d53e611/ changeset: r5037:d5ce1d53e611 user: guru date: 2011-02-10 16:33:08 summary: Better handling of complex interrupted microsatellites in 'Extract orthologous microsatellites for multiple species alignments' tool. affected #: 2 files (2.6 KB) --- a/tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.pl Wed Feb 09 16:49:43 2011 -0500 +++ b/tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.pl Thu Feb 10 10:33:08 2011 -0500 @@ -18,7 +18,12 @@ #------------------------------------------------------------------------------- # WHICH SPUTNIK USED? my $sputnikpath = (); -$sputnikpath = "sputnik" ; +$sputnikpath = "/Users/ydk/work/rhesus_microsat/codes/./sputnik_Mac-PowerPC"; +#print "sputnik_Mac-PowerPC non-existant\n" if !-e $sputnikpath; +#exit if !-e $sputnikpath; +#$sputnikpath = "bx-sputnik" ; +#print "ARGV input = @ARGV\n"; +#print "ARGV input :\n mafile=$mafile\n orthfile=$orthfile\n threshold_array=$threshold_array\n species_set=$species_set\n tree_definition=$tree_definition\n separation=$separation\n"; #------------------------------------------------------------------------------- # RUNFILE #------------------------------------------------------------------------------- @@ -37,9 +42,12 @@ my $tdir = tempdir( CLEANUP => 0 ); chdir $tdir; my $dir = getcwd; +#print "current dit=$dir\n"; #------------------------------------------------------------------------------- # CREATE AXT FILES IN FORWARD AND REVERSE ORDERS IF NECESSARY my @chrfiles=(); + +#my $mafile = "/Users/ydk/work/rhesus_microsat/results/galay/align.txt"; #$ARGV[0]; my $chromt=int(rand(10000)); my $p_chr=$chromt; @@ -54,20 +62,27 @@ push @exactspecies, $spec if $spec eq $espec; } } +#print "exactspecies=@exactspecies\n"; my $focalspec = $exactspecies[0]; my $arranged_species_set=join(".",@exactspecies); my $chr_name = join(".",("chr".$p_chr),$arranged_species_set, "net", "axt"); +#print "sending to maftoAxt_multispecies: $mafile, $tree_definition, $chr_name, $species_set .. focalspec=$focalspec \n"; maftoAxt_multispecies($mafile, $tree_definition, $chr_name, $species_set); +#print "done maf to axt conversion\n"; my $reverse_chr_name = join(".",("chr".$p_chr."r"),$arranged_species_set, "net", "axt"); artificial_axdata_inverter ($chr_name, $reverse_chr_name); +#print "reverse_chr_name=$reverse_chr_name\n"; #------------------------------------------------------------------------------- +# FIND THE CORRESPONDING CHIMP CHROMOSOME FROM FILE ORTp_chrS.TXT foreach my $direct ("reverse_direction","forward_direction"){ $p_chr=$chromt; + #print "direction = $direct\n"; $p_chr = $p_chr."r" if $direct eq "reverse_direction"; $p_chr = $p_chr if $direct eq "forward_direction"; my $config = $species_set; $config=~s/,/./g; my @orgs = split(/\./,$arranged_species_set); + #print "ORGS= @orgs\n"; my @tag=@orgs; @@ -80,6 +95,7 @@ my $ptag = $orgs[0]."-".$pchr.".".join(".",@orgs[1 ... scalar(@orgs)-1])."-".$threshold_array; my @sp_tags = (); + #print "orgs=@orgs, pchr=$pchr, hence, ptag = $ptag\n"; foreach my $sp (@tag){ push(@sp_tags, ($sp.".".$ptag)); } @@ -105,6 +121,10 @@ push(@title_queries, $title); } my $title_query = join($sep, @title_queries); + #print "title_queries=@title_queries\n"; + #print "query = >$title_query<\n"; + #print "orgs = @orgs\n"; + #------------------------------------------------------------------------------- # GET AXTNET FILES, EDIT THEM AND SPLIT THEM INTO HUMAN AND CHIMP INPUT FILES my $t1input = $pchr.".".$arranged_species_set.".net.axt"; @@ -115,6 +135,8 @@ } multi_species_t1($t1input,$tags,(join(",", @t1outputs)), $title_query); + #print "t1outputs=@t1outputs\n"; + #print "done t1\n"; #------------------------------------------------------------------------------- #START T2.PL @@ -261,6 +283,7 @@ multispecies_filtering_compound_microsats($compound_microsats, $compound_filterout, $compound_residue,$threshold_array,$threshold_array,scalar(@sp_tags)); $species_counter++; } + #print "done filtering both simple and compound microsatellites \n"; #------------------------------------------------------------------------------- @@ -289,6 +312,7 @@ } $sp_counter++; } + #print "\ndone grouping interrupted & simple microsats based on their motif size for further extention\n"; #------------------------------------------------------------------------------- # BREAK CHROMOSOME INTO PARTS OF CERTAIN NO. CONTIGS EACH, FOR FUTURE SEARCHING OF INTERRUPTED MICROSATELLITES @@ -311,6 +335,7 @@ my @unionarray = (); + #print "splist=@splist\n"; #------------------------------------------------------------------------------- # FIND INTERRUPTED MICROSATELLITES @@ -426,6 +451,7 @@ #xxxxxxx maftoAxt_multispecies xxxxxxx xxxxxxx maftoAxt_multispecies xxxxxxx xxxxxxx maftoAxt_multispecies xxxxxxx sub maftoAxt_multispecies { + #print "in maftoAxt_multispecies : got @_\n"; my $fname=$_[0]; open(IN,"<$_[0]") or die "Cannot open $_[0]: $! \n"; my $treedefinition = $_[1]; @@ -443,6 +469,7 @@ push @exactspecies, $spec if $spec eq $espec; } } + #print "exactspecies=@exactspecies\n"; ########### my $select = 2; @@ -453,7 +480,9 @@ my @allowedset = (); @allowedset = split(/;/,allowedSetOfSpecies(join("_",@species))) if $select == 0; @allowedset = join("_",0,@species) if $select == 1; + #print "species = @species , allowedset =",join("\n", @allowedset) ," \n"; @allowedset = join("_",0,@exactspecies) if $select == 2; + #print "allowedset = @allowedset and exactspecies = @exactspecies\n"; my $start = 0; my @sequences = (); @@ -474,6 +503,7 @@ } if ($line =~ /^s /){ + # print "fields1 = $fields[1] , start = $start\n"; foreach my $sp (@species){ if ($fields[1] =~ /$sp/){ @@ -493,12 +523,14 @@ my $arrno = 0; foreach my $set (@allowedset){ if ($arranged eq $set){ + # print "$arranged == $set\n"; $stopper = 0; last; } $arrno++; } if ($stopper == 0) { + # print " accepted\n"; @titles = split ";", orderInfo(join(";", @titles), $species_counter, $arranged) if $species_counter ne $arranged; @sequences = split ";", orderInfo(join(";", @sequences), $species_counter, $arranged) if $species_counter ne $arranged; my $filteredseq = filter_gaps(@sequences); @@ -519,6 +551,7 @@ } } +# print "countermatch = $countermatch\n"; } sub reorderSpecies{ @@ -535,6 +568,7 @@ sub filter_gaps{ my @sequences = @_; +# print "sequences sent are @sequences\n"; my $seq_length = length($sequences[0]); my $seq_no = scalar(@sequences); my $allgaps = (); @@ -557,7 +591,9 @@ for my $u (0 ... $#seq_array){ $bases = $bases.$seq_array[$u][$g]; } +# print $bases, "\n"; if ($bases eq $allgaps){ +# print "bases are $bases, position is $g \n"; for my $seq (@seq_array){ splice(@$seq , $g, 1); } @@ -580,6 +616,7 @@ sub allowedSetOfSpecies{ my @allowed_species = split(/_/,$_[0]); unshift @allowed_species, 0; +# print "allowed set = @allowed_species \n"; my @output = (); for (0 ... scalar(@allowed_species) - 4){ push(@output, join("_",@allowed_species)); @@ -626,14 +663,15 @@ my @fields = split(/\s*/,$line); $final_line = join("",reverse(@fields)); - print colored ['red'], "$line\n$final_line\n" if $final_line eq $line && $line !~ /chr/ && $line =~ /[a-zA-Z]/; + # print colored ['red'], "$line\n$final_line\n" if $final_line eq $line && $line !~ /chr/ && $line =~ /[a-zA-Z]/; # $trycounter++; + # print "trying again....$trycounter : $final_line\n" if $final_line eq $line; # } } - print colored ['yellow'], "$line\n$final_line\n" if $final_line eq $line && $line !~ /chr/ && $line =~ /[a-zA-Z]/; + # print colored ['yellow'], "$line\n$final_line\n" if $final_line eq $line && $line !~ /chr/ && $line =~ /[a-zA-Z]/; if ($line =~ /^[0-9]/){ - $line =~ s/chr([0-9a-b]+)/chr$1r/g; + $line =~ s/chr([A-Z0-9a-b]+)/chr$1r/g; $final_line = $line; } print OUT $final_line,"\n"; @@ -649,7 +687,7 @@ sub multi_species_t1 { my $input1 = $_[0]; - #print "@_\n"; #<STDIN>; +# print "@_\n"; #<STDIN>; my @tags = split(/_/, $_[1]); my @outputs = split(/,/, $_[2]); my $title_query = $_[3]; @@ -1678,7 +1716,7 @@ $key = join("\t",$1, $2, $3, $4, $5, $6, $7, $8, $9, $10, $11, $12); } else{ - print "no key in $sine\nfor pattern ([a-z0-9A-Z]+) (chr[0-9a-zA-Z]+) ([0-9]+) ([0-9]+) [\+|\-] (a-z0-9A-Z) (chr[0-9a-zA-Z]+) ([0-9]+) ([0-9]+) [\+|\-] (a-z0-9A-Z) (chr[0-9a-zA-Z]+) ([0-9]+) ([0-9]+) / \n"; +# print "no key in $sine\nfor pattern ([a-z0-9A-Z]+) (chr[0-9a-zA-Z]+) ([0-9]+) ([0-9]+) [\+|\-] (a-z0-9A-Z) (chr[0-9a-zA-Z]+) ([0-9]+) ([0-9]+) [\+|\-] (a-z0-9A-Z) (chr[0-9a-zA-Z]+) ([0-9]+) ([0-9]+) / \n"; } if (exists $micros{$key}){ @@ -1686,8 +1724,8 @@ delete $micros{$key}; foreach my $line (@microstring){ - print "#---------#---------#---------#---------#---------#---------#---------#---------\n" if $printer == 1; - print "microsat = $line" if $printer == 1; +# print "#---------#---------#---------#---------#---------#---------#---------#---------\n" if $printer == 1; +# print "microsat = $line" if $printer == 1; $linecounter++; my $copy_line = $line; my @mields = split(/\t/,$line); @@ -1704,7 +1742,7 @@ my @microields = split(/\][a-zA-Z|-]*\[/,$microsatcopy); my @inields = split(/\[[a-zA-Z|-]*\]/,$microsat); my $absolutstart = 1; my $absolutend = $absolutstart + ($end-$start); - print "absolut: start = $absolutstart, end = $absolutend\n" if $printer == 1; +# print "absolut: start = $absolutstart, end = $absolutend\n" if $printer == 1; shift @inields; #print "inields =@inields<\n"; $motifline =~ s/^\[|\]$//gs; @@ -1790,11 +1828,11 @@ if ($rightstopper == 1 && $leftstopper == 1){ print COMP $line; - print "rightstopper == 1 && leftstopper == 1\n" if $printer == 1; +# print "rightstopper == 1 && leftstopper == 1\n" if $printer == 1; next; } - print "pased initial testing phase \n" if $printer == 1; +# print "pased initial testing phase \n" if $printer == 1; my @outputs = (); my @orig_starts = (); my @orig_ends = (); @@ -1845,7 +1883,7 @@ while($lefter == 1){ $newline = left_extender($templine, $seq,$org); - print "returned line from left extender= $newline \n" if $printer == 1; +# print "returned line from left extender= $newline \n" if $printer == 1; if ($newline eq $templine){$templine = $newline; last;} else {$templine = $newline;} @@ -1853,7 +1891,7 @@ } while($righter == 1){ $newline = right_extender($templine, $seq,$org); - print "returned line from right extender= $newline \n" if $printer == 1; +# print "returned line from right extender= $newline \n" if $printer == 1; if ($newline eq $templine){$templine = $newline; last;} else {$templine = $newline;} if (right_extention_permission_giver($templine) eq "no") {last;} @@ -1864,7 +1902,7 @@ my @tempmotields = split(/\]\[/,$tempfields[$motifcord]); if (scalar(@tempmotields) == 1 && $templine eq $orig_templine) { - print "scalar ( tempmotields) = 1\n" if $printer == 1; +# print "scalar ( tempmotields) = 1\n" if $printer == 1; next; } my $prevmotif = shift(@tempmotields); @@ -1877,7 +1915,7 @@ $prevmotif = $tempmot; } if ( $stopper == 1) { - print "length tempmot != length prevmotif\n" if $printer == 1; +# print "length tempmot != length prevmotif\n" if $printer == 1; next; } my $lastend = 0; @@ -1886,32 +1924,32 @@ my $left_bp = (); my $right_bp = (); # print "new startcord = $tempfields[$startcord] , new endcord = $tempfields[$endcord].. orig strts = @orig_starts and orig ends = @orig_ends\n"; for my $o (0 ... $#orig_starts){ - print "we are talking abut tempstart:$tempfields[$startcord] >= origstart:$lastend && tempstart:$tempfields[$startcord] <= origend: $orig_ends[$o] \n" if $printer == 1; - print "we are talking abut tempend:$tempfields[$endcord] >= origstart:$lastend && tempstart:$tempfields[$endcord] >= origend: $orig_ends[$o] \n" if $printer == 1; +# print "we are talking abut tempstart:$tempfields[$startcord] >= origstart:$lastend && tempstart:$tempfields[$startcord] <= origend: $orig_ends[$o] \n" if $printer == 1; +# print "we are talking abut tempend:$tempfields[$endcord] >= origstart:$lastend && tempstart:$tempfields[$endcord] >= origend: $orig_ends[$o] \n" if $printer == 1; if (($tempfields[$startcord] > $lastend) && ($tempfields[$startcord] <= $orig_ends[$o])){ # && ($tempfields[$startcord] != $fields[$startcord]) - print "motif captured on left is $microields[$o] from $microsat\n" if $printer == 1; +# print "motif captured on left is $microields[$o] from $microsat\n" if $printer == 1; $left_captured = $o; $left_bp = $orig_ends[$o] - $tempfields[$startcord] + 1; } elsif ($tempfields[$endcord] > $lastend && $tempfields[$endcord] <= $orig_ends[$o]){ #&& $tempfields[$endcord] != $fields[$endcord]) - print "motif captured on right is $microields[$o] from $microsat\n" if $printer == 1; +# print "motif captured on right is $microields[$o] from $microsat\n" if $printer == 1; $right_captured = $o; $right_bp = $tempfields[$endcord] - $orig_starts[$o] + 1; } $lastend = $orig_ends[$o] } - print "leftcaptured = $left_captured, right = $right_captured\n" if $printer==1; +# print "leftcaptured = $left_captured, right = $right_captured\n" if $printer==1; my $leftmotif = (); my $left_trashed = (); if ($tempfields[$startcord] != $fields[$startcord]) { $leftmotif = $motields[$left_captured]; - print "$left_captured in @microields: $motields[$left_captured]\n" if $printer == 1; +# print "$left_captured in @microields: $motields[$left_captured]\n" if $printer == 1; if ( $left_captured !~ /[0-9]+/) {print $line,"\n", $templine,"\n"; } $left_trashed = length($microields[$left_captured]) - $left_bp; } my $rightmotif = (); my $right_trashed = (); if ($tempfields[$endcord] != $fields[$endcord]) { - print "$right_captured in @microields: $motields[$right_captured]\n" if $printer == 1; +# print "$right_captured in @microields: $motields[$right_captured]\n" if $printer == 1; $rightmotif = $motields[$right_captured]; $right_trashed = length($microields[$right_captured]) - $right_bp; } @@ -1920,54 +1958,54 @@ $stopper = 0; my $deletioner = 0; #if($tempfields[$startcord] != $fields[$startcord]){ - print "enter left: tempfields,startcord : $tempfields[$startcord] != $absolutstart && left_captured: $left_captured != 0 \n" if $printer==1; +# print "enter left: tempfields,startcord : $tempfields[$startcord] != $absolutstart && left_captured: $left_captured != 0 \n" if $printer==1; if ($left_captured != 0){ - print "at line 370, going: 0 ... $left_captured-1 \n" if $printer == 1; +# print "at line 370, going: 0 ... $left_captured-1 \n" if $printer == 1; for my $e (0 ... $left_captured-1){ if( length($motields[$e]) > 2 && length($microields[$e]) > (3* length($motields[$e]) )){ - print "motif on left not included too big to be ignored : $microields[$e] \n" if $printer == 1; +# print "motif on left not included too big to be ignored : $microields[$e] \n" if $printer == 1; $deletioner++; last; } if( length($motields[$e]) == 2 && length($microields[$e]) > (3* length($motields[$e]) )){ - print "motif on left not included too big to be ignored : $microields[$e] \n" if $printer == 1; +# print "motif on left not included too big to be ignored : $microields[$e] \n" if $printer == 1; $deletioner++; last; } if( length($motields[$e]) == 1 && length($microields[$e]) > (4* length($motields[$e]) )){ - print "motif on left not included too big to be ignored : $microields[$e] \n" if $printer == 1; +# print "motif on left not included too big to be ignored : $microields[$e] \n" if $printer == 1; $deletioner++; last; } } } #} - print "after left search, deletioner = $deletioner\n" if $printer == 1; +# print "after left search, deletioner = $deletioner\n" if $printer == 1; if ($deletioner >= 1) { - print "deletioner = $deletioner\n" if $printer == 1; +# print "deletioner = $deletioner\n" if $printer == 1; next; } $deletioner = 0; #if($tempfields[$endcord] != $fields[$endcord]){ - print "if tempfields endcord: $tempfields[$endcord] != absolutend: $absolutend\n and $right_captured != $#microields\n" if $printer==1; +# print "if tempfields endcord: $tempfields[$endcord] != absolutend: $absolutend\n and $right_captured != $#microields\n" if $printer==1; if ($right_captured != $#microields){ - print "at line 394, going: $right_captured+1 ... $#microields \n" if $printer == 1; +# print "at line 394, going: $right_captured+1 ... $#microields \n" if $printer == 1; for my $e ($right_captured+1 ... $#microields){ if( length($motields[$e]) > 2 && length($microields[$e]) > (3* length($motields[$e])) ){ - print "motif on right not included too big to be ignored : $microields[$e] \n" if $printer == 1; +# print "motif on right not included too big to be ignored : $microields[$e] \n" if $printer == 1; $deletioner++; last; } if( length($motields[$e]) == 2 && length($microields[$e]) > (3* length($motields[$e]) )){ - print "motif on right not included too big to be ignored : $microields[$e] \n" if $printer == 1; +# print "motif on right not included too big to be ignored : $microields[$e] \n" if $printer == 1; $deletioner++; last; } if( length($motields[$e]) == 1 && length($microields[$e]) > (4* length($motields[$e]) )){ - print "motif on right not included too big to be ignored : $microields[$e] \n" if $printer == 1; +# print "motif on right not included too big to be ignored : $microields[$e] \n" if $printer == 1; $deletioner++; last; } } } #} - print "deletioner = $deletioner\n" if $printer == 1; +# print "deletioner = $deletioner\n" if $printer == 1; if ($deletioner >= 1) { next; } @@ -1977,24 +2015,24 @@ if ($tempfields[$startcord] != $fields[$startcord] ){ #print "in left params: (length($leftmotif) == 1 && $tempfields[$startcord] != $fields[$startcord]) ... and .... $left_trashed > (1.5* length($leftmotif]) && ($tempfields[$startcord] != $fields[$startcord])\n"; if (length($leftmotif) == 1 && $left_trashed > 3){ - print "invaded left motif is long mononucleotide" if $printer == 1; +# print "invaded left motif is long mononucleotide" if $printer == 1; next; } elsif ((length($leftmotif) != 1 && $left_trashed > ( thrashallow($leftmotif)) && ($tempfields[$startcord] != $fields[$startcord]) ) ){ - print "invaded left motif too long" if $printer == 1; +# print "invaded left motif too long" if $printer == 1; next; } } if ($tempfields[$endcord] != $fields[$endcord] ){ #print "in right params: after $tempfields[$endcord] != $fields[$endcord] ..... (length($rightmotif)==1 && $tempfields[$endcord] != $fields[$endcord]) ... and ... $right_trashed > (1.5* length($rightmotif))\n"; if (length($rightmotif)==1 && $right_trashed){ - print "invaded right motif is long mononucleotide" if $printer == 1; +# print "invaded right motif is long mononucleotide" if $printer == 1; next; } elsif (length($rightmotif) !=1 && ($right_trashed > ( thrashallow($rightmotif)) && $tempfields[$endcord] != $fields[$endcord])){ - print "invaded right motif too long" if $printer == 1; +# print "invaded right motif too long" if $printer == 1; next; } @@ -2286,8 +2324,8 @@ ##print "scalar of fields = ",scalar(@fields),"\n"; if (exists ($fields[$motifcord+1])){ - print " print fields = @fields.. scalar=", scalar(@fields),".. motifcord+1 = $motifcord + 1 \n " if !exists $fields[$motifcord+1]; - <STDIN> if !exists $fields[$motifcord+1]; +# print " print fields = @fields.. scalar=", scalar(@fields),".. motifcord+1 = $motifcord + 1 \n " if !exists $fields[$motifcord+1]; +# <STDIN> if !exists $fields[$motifcord+1]; $fields[$motifcord+1] = $fields[$motifcord+1].",indel/deletion"; } else{$fields[$motifcord+1] = "indel/deletion";} @@ -2302,7 +2340,7 @@ my @seventeen=(); if (exists ($fields[$motifcord+3])){ ##print "at 608 we are doing this:length($microsat)+$intervalposs[$nikaal]\n"; - print " print fields = @fields\n " if !exists $fields[$motifcord+3]; +# print " print fields = @fields\n " if !exists $fields[$motifcord+3]; <STDIN> if !exists $fields[$motifcord+3]; my $currpos = length($microsat)+$intervalposs[$nikaal]; $fields[$motifcord+3] = $fields[$motifcord+3].",".$currpos; @@ -2596,7 +2634,7 @@ open(SUB,">$subset"); print SUB $sine; print OUT $subset,"\n"; - print $subset,"\n"; + # print $subset,"\n"; } } close OUT; @@ -2684,7 +2722,7 @@ my @microstring = @{$micros{$key}}; delete $micros{$key}; my @filteredmicrostring; - print "sequence = $sields[$sequencepos]" if $prinkter == 1; +# print "sequence = $sields[$sequencepos]" if $prinkter == 1; foreach my $line (@microstring){ $linecounter++; my $copy_line = $line; @@ -2692,7 +2730,7 @@ my $start = $fields[$startcord]; my $end = $fields[$endcord]; - print $line if $prinkter == 1; +# print $line if $prinkter == 1; #LOOKING FOR LEFTWARD EXTENTION OF MICROSATELLITE my $newline; while(1){ @@ -2704,7 +2742,7 @@ else {$line = $newline;} if (multiSpecies_interruptedMicrosatHunter_left_extention_permission_giver($line) eq "no") {last;} - print "returned line from left extender= $line \n" if $prinkter == 1; +# print "returned line from left extender= $line \n" if $prinkter == 1; } while(1){ # print "sequence = $sields[$sequencepos]\n" if $prinkter == 1; @@ -2715,9 +2753,9 @@ else {$line = $newline;} if (multiSpecies_interruptedMicrosatHunter_right_extention_permission_giver($line) eq "no") {last;} - print "returned line from right extender= $line \n" if $prinkter == 1; +# print "returned line from right extender= $line \n" if $prinkter == 1; } - print "\n>>>>>>>>>>>>>>>>\n In the end, the line is: \n$line\n<<<<<<<<<<<<<<<<\n" if $prinkter == 1; +# print "\n>>>>>>>>>>>>>>>>\n In the end, the line is: \n$line\n<<<<<<<<<<<<<<<<\n" if $prinkter == 1; my @tempfields = split(/\t/,$line); if ($tempfields[$microsatcord] =~ /\[/){ @@ -2744,7 +2782,7 @@ sub multiSpecies_interruptedMicrosatHunter_left_extender{ my ($line, $seq, $org) = @_; - print "left extender, like passed = $line\n" if $prinkter == 1; +# print "left extender, like passed = $line\n" if $prinkter == 1; # print "in left extender... line passed = $line and sequence is $seq\n" if $prinkter == 1; chomp $line; my @fields = split(/\t/,$line); @@ -2763,7 +2801,7 @@ } else {$firstmotif = $motif;} - print "hacked microsat = $microsat, motif = $motif, firstmotif = $firstmotif\n" if $prinkter == 1; +# print "hacked microsat = $microsat, motif = $motif, firstmotif = $firstmotif\n" if $prinkter == 1; my $leftphase = substr($microsat, 0,length($firstmotif)); my $phaser = $leftphase.$leftphase; my @phase = split(/\s*/,$leftphase); @@ -2779,7 +2817,7 @@ my $end = $rend; my $leftseq = substr($seq, 0, $start); - print "left phases are @phases , start = $start left sequence = ",substr($leftseq, -10),"\n" if $prinkter == 1; +# print "left phases are @phases , start = $start left sequence = ",substr($leftseq, -10),"\n" if $prinkter == 1; my @extentions = (); my @trappeds = (); my @intervalposs = (); @@ -2788,15 +2826,15 @@ my @intervals = (); my $firstmotif_length = length($firstmotif); foreach my $phase (@phases){ - print "left phase\t",substr($leftseq, -10),"\t$phase\n" if $prinkter == 1; - print "search patter = (($phase)+([a-zA-Z|-]{0,$firstmotif_length})) \n" if $prinkter == 1; +# print "left phase\t",substr($leftseq, -10),"\t$phase\n" if $prinkter == 1; +# print "search patter = (($phase)+([a-zA-Z|-]{0,$firstmotif_length})) \n" if $prinkter == 1; if ($leftseq =~ /(($phase)+([a-zA-Z|-]{0,$firstmotif_length}))$/i){ - print "in left pattern\n" if $prinkter == 1; +# print "in left pattern\n" if $prinkter == 1; my $trapped = $1; my $trappedpos = length($leftseq)-length($trapped); my $interval = $3; my $intervalpos = index($trapped, $interval) + 1; - print "left trapped = $trapped, interval = $interval, intervalpos = $intervalpos\n" if $prinkter == 1; +# print "left trapped = $trapped, interval = $interval, intervalpos = $intervalpos\n" if $prinkter == 1; my $extention = substr($trapped, 0, length($trapped)-length($interval)); my $leftpeep = substr($seq, 0, ($start-length($trapped))); @@ -2804,12 +2842,12 @@ for my $i (1 ... length($phase)-1){ my $overhang = substr($phase, -length($phase)+$i); - print "current overhang = $overhang, leftpeep = ",substr($leftpeep,-10)," whole sequence = ",substr($seq, ($end - ($end-$start) - 20), (($end-$start)+20)),"\n" if $prinkter == 1; +# print "current overhang = $overhang, leftpeep = ",substr($leftpeep,-10)," whole sequence = ",substr($seq, ($end - ($end-$start) - 20), (($end-$start)+20)),"\n" if $prinkter == 1; #TEMPORARY... BETTER METHOD NEEDED $leftpeep =~ s/-//g; if ($leftpeep =~ /$overhang$/i){ push(@passed_overhangs,$overhang); - print "l overhang\n" if $prinkter == 1; +# print "l overhang\n" if $prinkter == 1; } } @@ -2817,17 +2855,17 @@ my $overhang = $passed_overhangs[longest_array_element(@passed_overhangs)]; $extention = $overhang.$extention; $trapped = $overhang.$trapped; - print "trapped extended to $trapped \n" if $prinkter == 1; +# print "trapped extended to $trapped \n" if $prinkter == 1; $trappedpos = length($leftseq)-length($trapped); } push(@extentions,$extention); - print "extentions = @extentions \n" if $prinkter == 1; +# print "extentions = @extentions \n" if $prinkter == 1; push(@trappeds,$trapped ); push(@intervalposs,length($extention)+1); push(@trappedposs, $trappedpos); - print "trappeds = @trappeds\n" if $prinkter == 1; +# print "trappeds = @trappeds\n" if $prinkter == 1; push(@trappedphases, substr($extention,0,length($phase))); push(@intervals, $interval); } @@ -2837,7 +2875,7 @@ ############################ my $nikaal = longest_array_element(@trappeds); my $nikaal = shortest_array_element(@intervals); - print "longest element found = $nikaal \n" if $prinkter == 1; +# print "longest element found = $nikaal \n" if $prinkter == 1; if ($fields[$motifcord] !~ /\[/i) {$fields[$motifcord] = "[".$fields[$motifcord]."]";} $fields[$motifcord] = "[".$trappedphases[$nikaal]."]".$fields[$motifcord]; @@ -2889,14 +2927,14 @@ if ($fields[$microsatcord] =~ /\[/){ $returnline = multiSpecies_interruptedMicrosatHunter_merge($returnline); } - print "finally left-extended line = ",$returnline,"\n" if $prinkter == 1; +# print "finally left-extended line = ",$returnline,"\n" if $prinkter == 1; return $returnline; } sub multiSpecies_interruptedMicrosatHunter_right_extender{ - print "right extender\n" if $prinkter == 1; +# print "right extender\n" if $prinkter == 1; my ($line, $seq, $org) = @_; - print "in right extender... line passed = $line\n" if $prinkter == 1; +# print "in right extender... line passed = $line\n" if $prinkter == 1; # print "line = $line, sequence = ",$seq, "\n" if $prinkter == 1; chomp $line; my @fields = split(/\t/,$line); @@ -2915,7 +2953,7 @@ } else {$temp_lastmotif = $motif;} my $lastmotif = substr($microsat,-length($temp_lastmotif)); - print "hacked microsat = $microsat, motif = $motif, lastmotif = $lastmotif\n" if $prinkter == 1; +# print "hacked microsat = $microsat, motif = $motif, lastmotif = $lastmotif\n" if $prinkter == 1; my $rightphase = substr($microsat, -length($lastmotif)); my $phaser = $rightphase.$rightphase; my @phase = split(/\s*/,$rightphase); @@ -2931,8 +2969,8 @@ my $end = $rend; my $rightseq = substr($seq, $end+1); - print "length of sequence = " ,length($seq), "the coordinate to start from = ", $end+1, "\n" if $prinkter == 1; - print "right phases are @phases , end = $end right sequence = ",substr($rightseq,0,10),"\n" if $prinkter == 1; +# print "length of sequence = " ,length($seq), "the coordinate to start from = ", $end+1, "\n" if $prinkter == 1; +# print "right phases are @phases , end = $end right sequence = ",substr($rightseq,0,10),"\n" if $prinkter == 1; my @extentions = (); my @trappeds = (); my @intervalposs = (); @@ -2941,15 +2979,15 @@ my @intervals = (); my $lastmotif_length = length($lastmotif); foreach my $phase (@phases){ - print "right phase\t$phase\t",substr($rightseq,0,10),"\n" if $prinkter == 1; - print "search patter = (([a-zA-Z|-]{0,$lastmotif_length})($phase)+) \n" if $prinkter == 1; +# print "right phase\t$phase\t",substr($rightseq,0,10),"\n" if $prinkter == 1; +# print "search patter = (([a-zA-Z|-]{0,$lastmotif_length})($phase)+) \n" if $prinkter == 1; if ($rightseq =~ /^(([a-zA-Z|-]{0,$lastmotif_length}?)($phase)+)/i){ - print "in right pattern\n" if $prinkter == 1; +# print "in right pattern\n" if $prinkter == 1; my $trapped = $1; my $trappedpos = $end+1; my $interval = $2; my $intervalpos = index($trapped, $interval) + 1; - print "trapped = $trapped, interval = $interval\n" if $prinkter == 1; +# print "trapped = $trapped, interval = $interval\n" if $prinkter == 1; my $extention = substr($trapped, length($interval)); my $rightpeep = substr($seq, ($end+length($trapped))+1); @@ -2960,17 +2998,17 @@ for my $i (1 ... length($phase)-1){ my $overhang = substr($phase,0, $i); - print "current extention = $extention, overhang = $overhang, rightpeep = ",substr($rightpeep,0,10),"\n" if $prinkter == 1; +# print "current extention = $extention, overhang = $overhang, rightpeep = ",substr($rightpeep,0,10),"\n" if $prinkter == 1; if ($rightpeep =~ /^$overhang/i){ push(@passed_overhangs, $overhang); - print "r overhang\n" if $prinkter == 1; +# print "r overhang\n" if $prinkter == 1; } } if (scalar(@passed_overhangs) > 0){ my $overhang = @passed_overhangs[longest_array_element(@passed_overhangs)]; $extention = $extention.$overhang; $trapped = $trapped.$overhang; - print "trapped extended to $trapped \n" if $prinkter == 1; +# print "trapped extended to $trapped \n" if $prinkter == 1; } push(@extentions,$extention); @@ -2979,7 +3017,7 @@ push(@trappeds,$trapped ); push(@intervalposs,$intervalpos); push(@trappedposs, $trappedpos); - print "trappeds = @trappeds\n" if $prinkter == 1; +# print "trappeds = @trappeds\n" if $prinkter == 1; push(@trappedphases, substr($extention,0,length($phase))); push(@intervals, $interval); } @@ -2989,7 +3027,7 @@ ################################### my $nikaal = longest_array_element(@trappeds); my $nikaal = shortest_array_element(@intervals); - print "longest element found = $nikaal \n" if $prinkter == 1; +# print "longest element found = $nikaal \n" if $prinkter == 1; if ($fields[$motifcord] !~ /\[/i) {$fields[$motifcord] = "[".$fields[$motifcord]."]";} $fields[$motifcord] = $fields[$motifcord]."[".$trappedphases[$nikaal]."]"; @@ -3032,7 +3070,7 @@ if ($fields[$microsatcord] =~ /\[/){ $returnline = multiSpecies_interruptedMicrosatHunter_merge($returnline); } - print "finally right-extended line = ",$returnline,"\n" if $prinkter == 1; +# print "finally right-extended line = ",$returnline,"\n" if $prinkter == 1; return $returnline; } @@ -3058,7 +3096,7 @@ #print "firststretch = $firststretch\n" if $prinkter == 1; } else {$firstmotif = $motif;$firststretch = $microsat;} - print "if length:firststretch - length($firststretch) < threshes length :firstmotif ($firstmotif) - $thresholds[length($firstmotif)]\n" if $prinkter == 1; +# print "if length:firststretch - length($firststretch) < threshes length :firstmotif ($firstmotif) - $thresholds[length($firstmotif)]\n" if $prinkter == 1; if (length($firststretch) < $thresholds[length($firstmotif)]){ return "no"; } @@ -3206,20 +3244,22 @@ } sub multiSpecies_interruptedMicrosatHunter_merge{ + $prinkter = 0; +# print "~~~~~~~~|||~~~~~~~~|||~~~~~~~~|||~~~~~~~~|||~~~~~~~~|||~~~~~~~~|||~~~~~~~~\n"; my $line = $_[0]; - print "sent for mering: $line \n" if $prinkter ==1; +# print "sent for mering: $line \n" if $prinkter ==1; my @mields = split(/\t/,$line); my @fields = @mields; my $microsat = allCaps($fields[$microsatcord]); my $motifline = allCaps($fields[$motifcord]); my $microsatcopy = $microsat; - print "microsat = $microsat|\n" if $prinkter ==1; +# print "microsat = $microsat|\n" if $prinkter ==1; $microsatcopy =~ s/^\[|\]$//sg; chomp $microsatcopy; my @microields = split(/\][a-zA-Z|-]*\[/,$microsatcopy); my @inields = split(/\[[a-zA-Z|-]*\]/,$microsat); shift @inields; - print "inields =",join("|",@inields)," microields = ",join("|",@microields)," and count of microields = ", $#microields,"\n" if $prinkter ==1; +# print "inields =",join("|",@inields)," microields = ",join("|",@microields)," and count of microields = ", $#microields,"\n" if $prinkter ==1; $motifline =~ s/^\[|\]$//sg; my @motields = split(/\]\[/,$motifline); my @firstmotifs = (); @@ -3228,7 +3268,7 @@ $firstmotifs[$i] = substr($microields[$i],0,length($motields[$i])); $lastmotifs[$i] = substr($microields[$i],-length($motields[$i])); } - print "firstmotif = @firstmotifs... lastmotif = @lastmotifs\n" if $prinkter ==1; +# print "firstmotif = @firstmotifs... lastmotif = @lastmotifs\n" if $prinkter ==1; my @mergelist = (); my @inter_poses = split(/,/,$fields[$interr_poscord]); my $no_of_interruptions = $fields[$no_of_interruptionscord]; @@ -3236,52 +3276,56 @@ my @interrtypes = split(/,/,$fields[$interrtypecord]); my $stopper = 0; for my $i (0 ... $#motields-1){ - print "studying connection of $motields[$i] and $motields[$i+1], i = $i in $microsat\n:$lastmotifs[$i] eq $firstmotifs[$i+1]?\n" if $prinkter ==1; +# print "studying connection of $motields[$i] and $motields[$i+1], i = $i in $microsat\n:$lastmotifs[$i] eq $firstmotifs[$i+1]?\n" if $prinkter ==1; if ((allCaps($lastmotifs[$i]) eq allCaps($firstmotifs[$i+1])) && (!exists $inields[$i] || $inields[$i] !~ /[a-zA-Z]/)){ $stopper = 1; push(@mergelist, ($i)."_".($i+1)); #<STDIN> if $prinkter ==1; } } - print "mergelist = @mergelist\n" if $prinkter ==1; +# print "mergelist = @mergelist\n" if $prinkter ==1; return $line if scalar(@mergelist) == 0; - print "merging @mergelist\n" if $prinkter ==1; +# print "merging @mergelist\n" if $prinkter ==1; # <STDIN> if $prinkter ==1; foreach my $merging (@mergelist){ my @sets = split(/_/, $merging); - print "sets = @sets\n" if $prinkter ==1; +# print "sets = @sets\n" if $prinkter ==1; my @tempmicro = (); my @tempmot = (); - print "for loop going from 0 ... ", $sets[0]-1, "\n" if $prinkter ==1; +# print "for loop going from 0 ... ", $sets[0]-1, "\n" if $prinkter ==1; for my $i (0 ... $sets[0]-1){ - print " adding pre- i = $i adding: microields= $microields[$i]. motields = $motields[$i], inields = |$inields[$i]|\n" if $prinkter ==1; +# print " adding pre- i = $i adding: microields= $microields[$i]. motields = $motields[$i], inields = |$inields[$i]|\n" if $prinkter ==1; push(@tempmicro, "[".$microields[$i]."]"); push(@tempmicro, $inields[$i]); push(@tempmot, "[".$motields[$i]."]"); - print "adding pre-motifs number $i\n" if $prinkter ==1; - print "tempmot = @tempmot, tempmicro = @tempmicro \n" if $prinkter ==1; +# print "adding pre-motifs number $i\n" if $prinkter ==1; +# print "tempmot = @tempmot, tempmicro = @tempmicro \n" if $prinkter ==1; } - print "tempmot = @tempmot, tempmicro = @tempmicro \n" if $prinkter ==1; - print "now pushing ", "[",$microields[$sets[0]]," and ",$microields[$sets[1]],"]\n" if $prinkter ==1; +# print "tempmot = @tempmot, tempmicro = @tempmicro \n" if $prinkter ==1; +# print "now pushing ", "[",$microields[$sets[0]]," and ",$microields[$sets[1]],"]\n" if $prinkter ==1; my $pusher = "[".$microields[$sets[0]].$microields[$sets[1]]."]"; +# print "middle is, from @motields - @sets, number 0 which is is\n"; +# print ": $motields[$sets[0]]\n"; push (@tempmicro, $pusher); push(@tempmot, "[".$motields[$sets[0]]."]"); - push (@tempmicro, $inields[$sets[1]]) if $sets[1] != $#microields; + push (@tempmicro, $inields[$sets[1]]) if $sets[1] != $#microields && exists $sets[1] && exists $inields[$sets[1]]; my $outcoming = -2; - print "tempmot = @tempmot, tempmicro = @tempmicro \n" if $prinkter ==1; - print "for loop going from ",$sets[1]+1, " ... ", $#microields, "\n" if $prinkter ==1; +# print "tempmot = @tempmot, tempmicro = @tempmicro \n" if $prinkter ==1; +# print "for loop going from ",$sets[1]+1, " ... ", $#microields, "\n" if $prinkter ==1; for my $i ($sets[1]+1 ... $#microields){ - print " adding post- i = $i adding: microields= $microields[$i]. motields = $motields[$i]\n" if $prinkter ==1; - push(@tempmicro, "[".$microields[$i]."]"); - push(@tempmicro, $inields[$i]) unless $i == $#microields; +# print " adding post- i = $i adding: microields= $microields[$i]. motields = $motields[$i]\n" if $prinkter ==1; + push(@tempmicro, "[".$microields[$i]."]") if exists $microields[$i]; + push(@tempmicro, $inields[$i]) unless $i == $#microields || !exists $inields[$i]; push(@tempmot, "[".$motields[$i]."]"); - print "adding post-motifs number $i\n" if $prinkter ==1; +# print "adding post-motifs number $i\n" if $prinkter ==1; $outcoming = $i; } +# print "____________________________________________________________________________\n"; + $prinkter = 0; $fields[$microsatcord] = join("",@tempmicro); $fields[$motifcord] = join("",@tempmot); - print "tempmot = @tempmot, tempmicro = @tempmicro . microsat = $fields[$microsatcord] and motif = $fields[$motifcord] \n" if $prinkter ==1; +# print "tempmot = @tempmot, tempmicro = @tempmicro . microsat = $fields[$microsatcord] and motif = $fields[$motifcord] \n" if $prinkter ==1; splice(@interrtypes, $sets[0], 1); $fields[$interrtypecord] = join(",",@interrtypes); @@ -3300,7 +3344,7 @@ else{ $line = join("\t", @fields); } - print "post merging, the line is $line\n" if $prinkter ==1; +# print "post merging, the line is $line\n" if $prinkter ==1; #<STDIN> if $stopper ==1; return $line; } @@ -3411,7 +3455,7 @@ while(my $sine = <SEQ>){ #<STDIN> if $sine =~ /16349128/; next if $sine !~ /[a-zA-Z0-9]/; - print "-" x 150, "\n" if $printer == 1; +# print "-" x 150, "\n" if $printer == 1; my @sields = split(/\t/,$sine); my @merged = (); @@ -3435,7 +3479,7 @@ # print "line no : $linecount\n"; my @raw_microstring = @{$fmicros{$key}}; my %starts = (); my %ends = (); - print colored ['yellow'],"unsorted, unfiltered microats = \n" if $printer == 1; foreach (@raw_microstring) {print colored ['blue'],$_,"\n" if $printer == 1;} +# print colored ['yellow'],"unsorted, unfiltered microats = \n" if $printer == 1; foreach (@raw_microstring) {print colored ['blue'],$_,"\n" if $printer == 1;} my @microstring=(); for my $u (0 ... $#raw_microstring){ my @tields = split(/\t/,$raw_microstring[$u]); @@ -3457,7 +3501,7 @@ # print "line no : $linecount\n"; my @raw_microstring = @{$rmicros{$key}}; my %starts = (); my %ends = (); - print colored ['yellow'],"unsorted, unfiltered microats = \n" if $printer == 1; foreach (@raw_microstring) {print colored ['blue'],$_,"\n" if $printer == 1;} +# print colored ['yellow'],"unsorted, unfiltered microats = \n" if $printer == 1; foreach (@raw_microstring) {print colored ['blue'],$_,"\n" if $printer == 1;} my @microstring=(); for my $u (0 ... $#raw_microstring){ my @tields = split(/\t/,$raw_microstring[$u]); @@ -3553,7 +3597,7 @@ my @mergedSet = (); # print "set of microsats = @microstring \n"; my @microstring = map { $_->[0] } sort custom map { [$_, split /\t/ ] } @microstring0; - print "microstring = ", join("\n",@microstring0) ," \n---->\n", join("\n", @microstring),"\n ,,+." if $printer == 1; +# print "microstring = ", join("\n",@microstring0) ," \n---->\n", join("\n", @microstring),"\n ,,+." if $printer == 1; #<STDIN> if $printer == 1; my @tempmicrostring = @microstring; foreach my $line (@tempmicrostring){ @@ -3567,7 +3611,7 @@ } my $firstflag = 'down'; while( my $line =shift(@microstring)){ - print "-----------\nline = $line \n" if $printer == 1; +# print "-----------\nline = $line \n" if $printer == 1; chomp $line; my @fields = split(/\t/,$line); my $start = $fields[$startcord]; @@ -3592,9 +3636,9 @@ my $endrank = 1; while( ($startflag eq "down") || ($endflag eq "down") ){ - print "prestart=$prestart, post end =$postend.. seqlen =", length($sequence)," firstflag = $firstflag \n" if $printer == 1; +# print "prestart=$prestart, post end =$postend.. seqlen =", length($sequence)," firstflag = $firstflag \n" if $printer == 1; if ( (($prestart < 0) && $firstflag eq "up") || (($postend > length($sequence) && $firstflag eq "up")) ){ - print "coming to the end of sequence,post end = $postend and sequence length =", length($sequence)," so exiting\n" if $printer == 1; +# print "coming to the end of sequence,post end = $postend and sequence length =", length($sequence)," so exiting\n" if $printer == 1; last; } @@ -3611,7 +3655,7 @@ chomp $startmicro; $flag = 'down'; $startrank++; - print "deleting $microend{$i}[0] and $microstart{$tields[$startcord]}[0]\n" if $printer == 1; +# print "deleting $microend{$i}[0] and $microstart{$tields[$startcord]}[0]\n" if $printer == 1; delete $microend{$i}; delete $microstart{$tields[$startcord]}; $end = $tields[$endcord]; @@ -3629,7 +3673,7 @@ if ($endflag eq "down"){ for my $i ($start ... $postend){ - print "$start ----> $i -----> $postend\n" if $printer == 1; +# print "$start ----> $i -----> $postend\n" if $printer == 1; if(exists $microstart{$i} ){ chomp $microstart{$i}[0]; if(exists $compoundhash{$microstart{$i}[0]}) {next;} @@ -3640,11 +3684,11 @@ $endrank++; chomp $endmicro; $flag = 'down'; - print "deleting $microend{$tields[$endcord]}[0]\n" if $printer == 1; +# print "deleting $microend{$tields[$endcord]}[0]\n" if $printer == 1; delete $microstart{$i} if exists $microstart{$i} ; delete $microend{$tields[$endcord]} if exists $microend{$tields[$endcord]}; - print "done\n" if $printer == 1; +# print "done\n" if $printer == 1; shift @microstring; $end = $tields[$endcord]; @@ -3656,25 +3700,25 @@ $flag = 'up'; $endflag = 'up'; } - print "out of the if\n" if $printer == 1; +# print "out of the if\n" if $printer == 1; } - print "out of the for\n" if $printer == 1; +# print "out of the for\n" if $printer == 1; } # print "for next turn, flag status: startflag = $startflag and endflag = $endflag \n"; } #end while( $flag eq "down") - print "compoundlines = @compoundlines \n" if $printer == 1; +# print "compoundlines = @compoundlines \n" if $printer == 1; if (scalar (@compoundlines) == 1){ push(@nonmerged, $line); } if (scalar (@compoundlines) > 1){ - print "FROM CLUSTERER\n" if $printer == 1; +# print "FROM CLUSTERER\n" if $printer == 1; push(@mergedSet,merge_microsats(@compoundlines, $sequence) ); } } #end foreach my $line (@microstring){ -print join("\n",@mergedSet),"<-----mergedSet\n" if $printer == 1; +# print join("\n",@mergedSet),"<-----mergedSet\n" if $printer == 1; #<STDIN> if scalar(@mergedSet) > 0; # print "EXIT: find_clusters\n"; return (join("_",@nonmerged). "=".join("_",@mergedSet)); @@ -3711,7 +3755,7 @@ my %forPopouting = (); while( my $line =shift(@merged)){ - print "\n MErgedline: $line \n" if $printer == 1; +# print "\n MErgedline: $line \n" if $printer == 1; chomp $line; my @fields = split(/\t/,$line); my $start = $fields[$startcord]; @@ -3764,7 +3808,7 @@ push(@mergedSet,join("\t",@compoundlines) ); } else { - print "FROM POPOUTER\n" if $printer == 1; +# print "FROM POPOUTER\n" if $printer == 1; push(@mergedSet, merge_microsats(@compoundlines, $sequence) ); } } @@ -3789,7 +3833,7 @@ $fields[$startcord] = $start; $fields[$endcord] = $end; $fields[$microsatcord] = reverse_micro($fields[$microsatcord]); - print "RETURNIG: ", join("\t",@fields), "\n" if $printer == 1; +# print "RETURNIG: ", join("\t",@fields), "\n" if $printer == 1; return join("\t",@fields); } @@ -3823,7 +3867,7 @@ my @fmerged = (); foreach my $micro (@merged) { my @fields = split(/\t/,$micro); - if ($fields[3] =~ /chr[0-9a-z]+r/){ + if ($fields[3] =~ /chr[A-Z0-9a-z]+r/){ my $key = join("_",$fields[1], $fields[$startcord], $fields[$endcord]); # print "adding ... \n$key\n$micro\n"; push(@{$revmerged{$key}}, $micro); @@ -3853,7 +3897,7 @@ sub invert_microsat{ my $micro = $_[0]; chomp $micro; - if ($micro =~ /chr[0-9a-z]+r/) { $micro =~ s/chr([0-9a-b]+)r/chr$1/g ;} + if ($micro =~ /chr[A-Z0-9a-z]+r/) { $micro =~ s/chr([0-9a-b]+)r/chr$1/g ;} else { $micro =~ s/chr([0-9a-b]+)/chr$1r/g ; } my $sequence = $_[1]; $sequence =~ s/ //g; @@ -4032,10 +4076,10 @@ foreach my $r (@localrs){ chomp $r; my @rields = split(/\t/,$r); - print "rields = @rields\n" if $printer == 1; +# print "rields = @rields\n" if $printer == 1; my $reciprocalstart = length($sequence) - $rields[$endcord] + 1; my $reciprocalend = length($sequence) - $rields[$startcord] + 1; - print "reciprocal start = $reciprocalstart = ",length($sequence)," - $rields[$endcord] + 1\n" if $printer == 1; +# print "reciprocal start = $reciprocalstart = ",length($sequence)," - $rields[$endcord] + 1\n" if $printer == 1; my $microsat = reverse_micro(all_caps($rields[$microsatcord])); my @localcollection=(); for my $i ($reciprocalstart+1 ... $reciprocalend-1){ @@ -4055,11 +4099,11 @@ } elsif (scalar(@localcollection) == 1){ - print "f microsat = $localcollection[0]\n" if $printer == 1; +# print "f microsat = $localcollection[0]\n" if $printer == 1; my @lields = split(/\t/,$localcollection[0]); $lields[$microsatcord]=all_caps($lields[$microsatcord]); - print "comparing: $microsat and $lields[$microsatcord]\n" if $printer == 1; - print "coordinates are: $lields[$startcord]-$lields[$endcord] and $reciprocalstart-$reciprocalend\n" if $printer == 1; +# print "comparing: $microsat and $lields[$microsatcord]\n" if $printer == 1; +# print "coordinates are: $lields[$startcord]-$lields[$endcord] and $reciprocalstart-$reciprocalend\n" if $printer == 1; if ($microsat eq $lields[$microsatcord]){ chomp $localcollection[0]; print SAME $localcollection[0], "\n"; @@ -4067,19 +4111,19 @@ if ($microsat ne $lields[$microsatcord]){ chomp $localcollection[0]; my $newmicro = microsatChooser(join("\t",@lields), join("\t",@rields), $sequence); - print "newmicro = $newmicro\n" if $printer == 1; +# print "newmicro = $newmicro\n" if $printer == 1; if ($newmicro =~ /[a-zA-Z]/){ print SAME $newmicro,"\n"; } else{ print DIFF join("\t",$localcollection[0],"-->",$rields[$typecord],$reciprocalstart,$reciprocalend, $rields[$microsatcord], reverse_micro($rields[$motifcord]), @rields[$motifcord+1 ... $#rields] ),"\n"; - print join("\t",$localcollection[0],"-->",$rields[$typecord],$reciprocalstart,$reciprocalend, $rields[$microsatcord], reverse_micro($rields[$motifcord]), @rields[$motifcord+1 ... $#rields] ),"\n" if $printer == 1; - print "@rields\n@lields\n" if $printer == 1; +# print join("\t",$localcollection[0],"-->",$rields[$typecord],$reciprocalstart,$reciprocalend, $rields[$microsatcord], reverse_micro($rields[$motifcord]), @rields[$motifcord+1 ... $#rields] ),"\n" if $printer == 1; +# print "@rields\n@lields\n" if $printer == 1; } } } else{ - print "multiple found for $r --> ", join("\t",@localcollection),"\n" if $printer == 1; +# print "multiple found for $r --> ", join("\t",@localcollection),"\n" if $printer == 1; } } } @@ -4146,13 +4190,13 @@ my $r_purestretch = join("",@r_microields); if ($fields[$typecord]=~/nucleotide/ && $rields[$typecord]=~/nucleotide/){ - print "now.. studying $forward\n$reverse\n" if $printer == 1; +# print "now.. studying $forward\n$reverse\n" if $printer == 1; if ($fields[$typecord] eq $rields[$typecord]){ - print "comparing motifs::", all_caps($fields[$motifcord]) ," and ", all_caps(reverse_micro($rields[$motifcord])), "\n" if $printer == 1; +# print "comparing motifs::", all_caps($fields[$motifcord]) ," and ", all_caps(reverse_micro($rields[$motifcord])), "\n" if $printer == 1; if(motifBYmotif_match(all_caps($fields[$motifcord]), all_caps(reverse_micro($rields[$motifcord]))) == 1){ my $subset_answer = isSubset($forward, $reverse, $seqLength); - print "subset answer = $subset_answer\n" if $printer == 1; +# print "subset answer = $subset_answer\n" if $printer == 1; return $forward if $subset_answer == 1; return invert_microsat($reverse, $sequence) if $subset_answer == 2; return $forward if $subset_answer == 0 && length($f_purestretch) >= length($r_purestretch); @@ -4202,13 +4246,13 @@ } } if ($fields[$typecord] eq "compound" && $rields[$typecord] eq "compound"){ - print "comparing compound motifs::", all_caps($fields[$motifcord]) ," and ", all_caps(reverse_micro($rields[$motifcord])), "\n" if $printer == 1; +# print "comparing compound motifs::", all_caps($fields[$motifcord]) ," and ", all_caps(reverse_micro($rields[$motifcord])), "\n" if $printer == 1; if(motifBYmotif_match(all_caps($fields[$motifcord]), all_caps(reverse_micro($rields[$motifcord]))) == 1){ my $subset_answer = isSubset($forward, $reverse, $seqLength); - print "subset answer = $subset_answer\n" if $printer == 1; +# print "subset answer = $subset_answer\n" if $printer == 1; return $forward if $subset_answer == 1; return invert_microsat($reverse, $sequence) if $subset_answer == 2; - print length($f_purestretch) ,">", length($r_purestretch)," \n" if $printer == 1; +# print length($f_purestretch) ,">", length($r_purestretch)," \n" if $printer == 1; return $forward if $subset_answer == 0 && length($f_purestretch) >= length($r_purestretch); return invert_microsat($reverse, $sequence) if $subset_answer == 0 && length($f_purestretch) < length($r_purestretch); if ($subset_answer == 3){ @@ -4243,11 +4287,11 @@ } if ($fields[$typecord] eq "compound" && $rields[$typecord] =~ /nucleotide/){ - print "one compound, one nucleotide\n" if $printer == 1; +# print "one compound, one nucleotide\n" if $printer == 1; return merge_microsats($forward, invert_microsat($reverse, $sequence), $sequence); } if ($fields[$typecord] =~ /nucleotide/ && $rields[$typecord]eq "compound"){ - print "one compound, one nucleotide\n" if $printer == 1; +# print "one compound, one nucleotide\n" if $printer == 1; return merge_microsats($forward, invert_microsat($reverse, $sequence), $sequence); } } @@ -4258,7 +4302,7 @@ my $seqLength = $_[2]; my $r_start = $seqLength - $rields[$endcord] + 1; my $r_end = $seqLength - $rields[$startcord] + 1; - print "we have $fields[$startcord] -> $fields[$endcord] && $r_start -> $r_end\n" if $printer == 1; +# print "we have $fields[$startcord] -> $fields[$endcord] && $r_start -> $r_end\n" if $printer == 1; return "0" if $fields[$startcord] == $r_start && $fields[$endcord] == $r_end; return "1" if $fields[$startcord] <= $r_start && $fields[$endcord] >= $r_end; return "2" if $r_start <= $fields[$startcord] && $r_end >= $fields[$endcord]; @@ -4284,7 +4328,7 @@ for my $i (0 ... $#sub){ my $probe = $sub[$i].$sub[$i]; - print "probing $probe and $mega[$i]\n" if $printer == 1; +# print "probing $probe and $mega[$i]\n" if $printer == 1; if ($probe =~ /$mega[$i]/) {$subresult = 1; } else {$subresult = 0; last; } } @@ -4416,7 +4460,7 @@ # print $key, "#-#-#-#-#-#-#-#\n"; if ($line =~ /([0-9]+)\s+([0-9a-zA-Z]+)\s(chr[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)\s/ ) { my $key = join("\t",$1, $2, $3, $4, $5); - print "key = $key\n" if $prinkter == 1; +# print "key = $key\n" if $prinkter == 1; push (@{$seen{$key}},$line); $microcounter++; } @@ -4424,7 +4468,7 @@ } } # print "done hash.. linecounter = $linecounter, microcounter = $microcounter and total keys entered = ",scalar(keys %seen),"\n"; - print INFO "done hash.. linecounter = $linecounter, microcounter = $microcounter and total keys entered = ",scalar(keys %seen),"\n"; +# print INFO "done hash.. linecounter = $linecounter, microcounter = $microcounter and total keys entered = ",scalar(keys %seen),"\n"; close SPUT; #---------------------------------------------------------------------------------------------------------------- @@ -4449,7 +4493,7 @@ my $keysused = 0; while (my $line = <MATCH>) { - print colored ['magenta'], $line if $prinkter == 1; +# print colored ['magenta'], $line if $prinkter == 1; next if $line !~ /[a-zA-Z0-9]/; chomp $line; my @fields2 = split(/\t/,$line); @@ -4458,10 +4502,10 @@ if ($line =~ /([0-9]+)\s+([0-9a-zA-Z]+)\s(chr[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)\s/ ) { $matchkeysformed++; $key2 = join("\t",$1, $2, $3, $4, $5); - print "key = $key2 \n" if $prinkter == 1; +# print "key = $key2 \n" if $prinkter == 1; } else{ - print "could not make ker in SEQ : $line\n"; +# print "could not make ker in SEQ : $line\n"; next; } my $sequence = $fields2[$sequencepos]; @@ -4473,7 +4517,7 @@ delete $seen{$key2}; my @sequencearr = split(/\s*/, $sequence); - print "sequencearr = @sequencearr\n" if $prinkter == 1; +# print "sequencearr = @sequencearr\n" if $prinkter == 1; my $counter; @@ -4487,13 +4531,13 @@ my @unsorted = (); my %starts = (); my %ends = (); - print colored ['yellow'],"unsorted, unfiltered microats = \n" if $prinkter == 1; foreach (@unsorted_raw) {print colored ['blue'],$_,"\n" if $prinkter == 1;} +# print colored ['yellow'],"unsorted, unfiltered microats = \n" if $prinkter == 1; foreach (@unsorted_raw) {print colored ['blue'],$_,"\n" if $prinkter == 1;} for my $u (0 ... $#unsorted_raw){ my @tields = split(/\t/,$unsorted_raw[$u]); next if exists $starts{$tields[$startcord]} && exists $ends{$tields[$endcord]}; push(@unsorted, $unsorted_raw[$u]); $starts{$tields[$startcord]} = $unsorted_raw[$u]; - print "in starts : $tields[$startcord] -> $unsorted_raw[$u]\n" if $prinkter == 1; +# print "in starts : $tields[$startcord] -> $unsorted_raw[$u]\n" if $prinkter == 1; } my $basecounter= 0; @@ -4517,7 +4561,7 @@ if (exists $starts{$basecounter}){ my $locus = $starts{$basecounter}; - print "locus identified = $locus\n" if $prinkter == 1; +# print "locus identified = $locus\n" if $prinkter == 1; my @fields3 = split(/\t/,$locus); my $start = $fields3[$startcord]; my $end = $fields3[$endcord]; @@ -4529,14 +4573,14 @@ my $leftbrackets=(); my $rightbrackets = (); my $micro_cpy = $microsat; - print "microsat = $microsat\n" if $prinkter == 1; +# print "microsat = $microsat\n" if $prinkter == 1; while($microsat =~ m/\[/g) {push(@leftbracketpos, (pos($microsat))); $leftbrackets = join("__",@leftbracketpos);$bracket_picker='yes';} while($microsat =~ m/\]/g) {push(@rightbracketpos, (pos($microsat))); $rightbrackets = join("__",@rightbracketpos);} $microsat =~ s/[\[\]\-\*]//g; - print "microsat = $microsat\n" if $prinkter == 1; +# print "microsat = $microsat\n" if $prinkter == 1; my $human_search = join '-*', split //, $microsat; my $temp = substr($sequence, $poscounter-1); - print "with poscounter = $poscounter\n" if $prinkter == 1; +# print "with poscounter = $poscounter\n" if $prinkter == 1; my $search_result = (); my $posnow = (); while ($temp =~ /($human_search)/gi){ @@ -4725,9 +4769,9 @@ if ($line =~ /([0-9]+)\s+($focalspec)\s(chr[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)/ ) { $key = join("\t",$1, $2, $4, $5); - print "key = : $key\n" if $prinkter == 1; +# print "key = : $key\n" if $prinkter == 1; - print $line if $prinkter == 1; +# print $line if $prinkter == 1; push (@{$single_hash{$key}},$line); } else{ @@ -4736,10 +4780,10 @@ } push @hasharr, {%single_hash}; # print "@{$single_hash{$key}} \n"; - print "done $path: counter = $counter\n" if $prinkter == 1; +# print "done $path: counter = $counter\n" if $prinkter == 1; close READ; } - #print "Done hashes\n"; +# print "Done hashes\n"; #---------------------------------------------------------------------------------------------------------------- my $question=(); #---------------------------------------------------------------------------------------------------------------- @@ -4754,22 +4798,24 @@ my %contigpath=(); my $dotcounter = 0; while (my $line = <BO>){ - print "x" x 60, "\n" if $prinkter == 1; +# print "x" x 60, "\n" if $prinkter == 1; $dotcounter++; - #print "." if $dotcounter % 100 ==0; - #print "\n" if $dotcounter % 5000 ==0; +# print "." if $dotcounter % 100 ==0; +# print "\n" if $dotcounter % 5000 ==0; next if $line !~ /^[0-9]+/; - print $line if $prinkter == 1; +# print $line if $prinkter == 1; chomp $line; my @fields2 = split(/\t/,$line); my $key2 = (); if ($line =~ /([0-9]+)\s+($focalspec)\s(chr[0-9a-zA-Z]+)\s([0-9]+)\s([0-9]+)/ ) { $key2 = join("\t",$1, $2, $4, $5); } - else {print "seq line $line incompatible\n" if $prinkter == 1; next;} + else { +# print "seq line $line incompatible\n" if $prinkter == 1; + next;} @@ -4809,22 +4855,22 @@ my @currentcontigchrs=(); for my $i (0 ... $#tags){ - print "searching for : if exists hasharr: $i : $tags[$i] : $key2 \n" if $prinkter == 1; +# print "searching for : if exists hasharr: $i : $tags[$i] : $key2 \n" if $prinkter == 1; my @temparr = (); if (exists $hasharr[$i]{$key2}){ @temparr = @{$hasharr[$i]{$key2}}; - print "in line $line, trying to hunt for: $tags[$i]\\s([a-zA-Z0-9])+\\s([0-9]+)\\s([0-9]+) \n" if $prinkter == 1; +# print "in line $line, trying to hunt for: $tags[$i]\\s([a-zA-Z0-9])+\\s([0-9]+)\\s([0-9]+) \n" if $prinkter == 1; $line =~ /$tags[$i]\s([a-zA-Z0-9]+)\s([0-9]+)\s([0-9]+)/; - print "org = $tags[$i], and chr = $1, start = $2, end =$3 \n" if $prinkter == 1; +# print "org = $tags[$i], and chr = $1, start = $2, end =$3 \n" if $prinkter == 1; my $startkey = $1."_".$2; print "adding start key for this alignmebt block: $startkey to species $tags[$i]\n" if $prinkter == 1; my $endkey = $1."_".$3; print "adding end key for this alignmebt block: $endkey to species $tags[$i]\n" if $prinkter == 1; $contigstarts[$i]{$startkey}= $key2; $contigends[$i]{$endkey}= $key2; - print "confirming existance: \n" if $prinkter == 1; - print "present \n" if exists $contigends[$i]{$endkey} && $prinkter == 1; - print "absent \n" if !exists $contigends[$i]{$endkey} && $prinkter == 1; +# print "confirming existance: \n" if $prinkter == 1; +# print "present \n" if exists $contigends[$i]{$endkey} && $prinkter == 1; +# print "absent \n" if !exists $contigends[$i]{$endkey} && $prinkter == 1; $currentcontigchrs[$i]=$1; $currentcontigstarts[$i]=$2; $currentcontigends[$i]=$3; @@ -4846,7 +4892,7 @@ # print "---------------------------\n"; foreach my $templine (@temparr){ - print "templine = $templine\n" if $prinkter == 1; +# print "templine = $templine\n" if $prinkter == 1; my @tields = split(/\t/,$templine); my $start = $tields[$startcord]; # - $tields[$gapcord]; my $end = $tields[$endcord]; #- $tields[$gapcord]; @@ -4870,7 +4916,7 @@ foreach my $cluster (@clusters) { my @constituenst = split(/,/,$cluster); - print "clusters returned: @constituenst\n" if $prinkter == 1; +# print "clusters returned: @constituenst\n" if $prinkter == 1; } @string = split("_",stringPainter(join("_",@string),$foundclusters)); @@ -4879,13 +4925,13 @@ } next if $stopper == 1; - print colored ['blue'],"FINAL:\n" if $prinkter == 1; +# print colored ['blue'],"FINAL:\n" if $prinkter == 1; my $finalclusters =findClusters(join("!",@string), 1); - print colored ['blue'],"----------------------\n" if $prinkter == 1; +# print colored ['blue'],"----------------------\n" if $prinkter == 1; my @clusters = split(/,/,$finalclusters); - print "@string\n" if $prinkter == 1; - print "@clusters\n" if $prinkter == 1; - print "------------------------------------------------------------------\n" if $prinkter == 1; +# print "@string\n" if $prinkter == 1; +# print "@clusters\n" if $prinkter == 1; +# print "------------------------------------------------------------------\n" if $prinkter == 1; my $clustno = 0; @@ -4921,7 +4967,7 @@ my $extremeend = largest_number(@ends); push(@contigClusterstarts, $extremestart); push(@contigClusterends, $extremeend); - print "cluster starts from $extremestart and ends at $extremeend \n" if $prinkter == 1 ; +# print "cluster starts from $extremestart and ends at $extremeend \n" if $prinkter == 1 ; foreach my $clustparts (@localclust){ my @pattern = split(/:/, $clustparts); @@ -4929,7 +4975,7 @@ push (@result, $starthash[$pattern[0]]{$pattern[1]}); } push(@contigcluster, join("\t", @result)); - print join("\t", @result),"<-result \n" if $prinkter == 1 ; +# print join("\t", @result),"<-result \n" if $prinkter == 1 ; } @@ -4940,7 +4986,7 @@ $contigclustersFirstStartOnly{$key2}=$firstclusterstart; $contigclustersLastEndOnly{$key2} = $lastclusterend; $contigclusters{$key2}=[ @contigcluster ]; - print "currentcontigchr are @currentcontigchrs , firstclusterstart = $firstclusterstart, lastclusterend = $lastclusterend\n " if $prinkter == 1; +# print "currentcontigchr are @currentcontigchrs , firstclusterstart = $firstclusterstart, lastclusterend = $lastclusterend\n " if $prinkter == 1; for my $i (0 ... $#tags){ #1 check if there exists adjacent alignment block wrt coordinates of this species. next if $currentcontigchrs[$i] eq "0"; #1 this means that there are no microsats in this species in this alignment block.. @@ -4951,7 +4997,7 @@ #3 adjacent alignment block is found lateron, the exact distance between the potentially #4 adjacent microsat clusters can be found here. the exact start coordinate will be used #5 immediately below. - print "full sequence = $origsequences[$i] and its length = ",length($origsequences[$i])," \n" if $prinkter == 1; + # print "full sequence = $origsequences[$i] and its length = ",length($origsequences[$i])," \n" if $prinkter == 1; my $species_startsubstring = substr($origsequences[$i], 0, $firstclusterstart); my $species_endsubstring = (); @@ -4959,8 +5005,8 @@ if (length ($origsequences[$i]) <= $lastclusterend+1){ $species_endsubstring = "";} else{ $species_endsubstring = substr($origsequences[$i], $lastclusterend+1);} - print "\nnot defined species_endsubstring...\n" if !defined $species_endsubstring && $prinkter == 1; - print "for species: $tags[$i]: \n" if $prinkter == 1; +# print "\nnot defined species_endsubstring...\n" if !defined $species_endsubstring && $prinkter == 1; +# print "for species: $tags[$i]: \n" if $prinkter == 1; $species_startsubstring =~ s/-| //g; $species_endsubstring =~ s/-| //g; @@ -4969,11 +5015,11 @@ - print "species_startsubstring = $species_startsubstring, and its length =",length($species_startsubstring)," \n" if $prinkter == 1; - print "species_endsubstring = $species_endsubstring, and its length =",length($species_endsubstring)," \n" if $prinkter == 1; - print "attaching to contigclustersLastEndOnly: $key2: $i\n" if $prinkter == 1; +# print "species_startsubstring = $species_startsubstring, and its length =",length($species_startsubstring)," \n" if $prinkter == 1; +# print "species_endsubstring = $species_endsubstring, and its length =",length($species_endsubstring)," \n" if $prinkter == 1; +# print "attaching to contigclustersLastEndOnly: $key2: $i\n" if $prinkter == 1; - print "just confirming: $contigclustersLastEndLengthOnly{$key2}[$i] \n" if $prinkter == 1; +# print "just confirming: $contigclustersLastEndLengthOnly{$key2}[$i] \n" if $prinkter == 1; } @@ -5001,7 +5047,7 @@ my $existing_removed=0; while (my $line = <BO>){ - print "x" x 60, "\n" if $prinkter == 1; +# print "x" x 60, "\n" if $prinkter == 1; next if $line !~ /^[0-9]+/; #print $line; chomp $line; @@ -5012,7 +5058,7 @@ } else {print "seq line $line incompatible\n"; next;} - print "KEY = : $key2\n" if $prinkter == 1; +# print "KEY = : $key2\n" if $prinkter == 1; my @currentcontigstarts=(); @@ -5024,9 +5070,9 @@ @clusters = @{$contigclusters{$key2}}; @clusterscopy=@clusters; for my $i (0 ... $#tags){ - print "in line $line, trying to hunt for: $tags[$i]\\s([a-zA-Z0-9])+\\s([0-9]+)\\s([0-9]+) \n" if $prinkter == 1; + # print "in line $line, trying to hunt for: $tags[$i]\\s([a-zA-Z0-9])+\\s([0-9]+)\\s([0-9]+) \n" if $prinkter == 1; if ($line =~ /$tags[$i]\s([a-zA-Z0-9]+)\s([0-9]+)\s([0-9]+)/){ - print "org = $tags[$i], and chr = $1, start = $2, end =$3 \n" if $prinkter == 1; + # print "org = $tags[$i], and chr = $1, start = $2, end =$3 \n" if $prinkter == 1; my $startkey = $1."_".$2; #print "adding start key for this alignmebt block: $startkey to species $tags[$i]\n" if $prinkter == 1; my $endkey = $1."_".$3; #print "adding end key for this alignmebt block: $endkey to species $tags[$i]\n" if $prinkter == 1; $currentcontigchrs[$i]=$1; @@ -5035,7 +5081,7 @@ } else { $currentcontigchrs[$i] = 0; - print "no microsat clusters for $key2\n" if $prinkter == 1; next; + # print "no microsat clusters for $key2\n" if $prinkter == 1; next; } } } # print "exists: @{$hasharr[$i]{$key2}}[0]\n"} @@ -5050,7 +5096,7 @@ next if scalar @currentcontigchrs == 0; - print "contigchrs= @currentcontigchrs \n" if $prinkter == 1; + # print "contigchrs= @currentcontigchrs \n" if $prinkter == 1; my %visitedcontigs=(); for my $i (0 ... $#tags){ @@ -5067,38 +5113,38 @@ my $lastclusterend = $contigclustersLastEndOnly{$key2}; my $key3 = $currentcontigchrs[$i]."_".($currentcontigstarts[$i]); - print "check if exists $key3 in contigends for $i\n" if $prinkter == 1; +# print "check if exists $key3 in contigends for $i\n" if $prinkter == 1; if (exists($contigends[$i]{$key3}) && !exists $visitedcontigs{$contigends[$i]{$key3}}){ $visitedcontigs{$contigends[$i]{$key3}} = $contigends[$i]{$key3}; #1 this array keeps track of adjacent contigs that we have already visited, thus saving computational time and potential redundancies# - print "just checking the hash visitedcontigs: ",$visitedcontigs{$contigends[$i]{$key3}} ,"\n" if $prinkter == 1; + # print "just checking the hash visitedcontigs: ",$visitedcontigs{$contigends[$i]{$key3}} ,"\n" if $prinkter == 1; #1 extract coordinates of the last cluster of this found alignment block - print "key of the found alignment block = ", $contigends[$i]{$key3},"\n" if $prinkter == 1; - print "we are trying to mine: contigclustersAllLastEndLengthOnly_raw: $contigends[$i]{$key3}: $i \n" if $prinkter == 1; - print "EXISTS\n" if exists $contigclusters{$contigends[$i]{$key3}} && $prinkter == 1; - print "does NOT EXIST\n" if !exists $contigclusters{$contigends[$i]{$key3}} && $prinkter == 1; +# print "key of the found alignment block = ", $contigends[$i]{$key3},"\n" if $prinkter == 1; + # print "we are trying to mine: contigclustersAllLastEndLengthOnly_raw: $contigends[$i]{$key3}: $i \n" if $prinkter == 1; + # print "EXISTS\n" if exists $contigclusters{$contigends[$i]{$key3}} && $prinkter == 1; + # print "does NOT EXIST\n" if !exists $contigclusters{$contigends[$i]{$key3}} && $prinkter == 1; my @contigclustersAllFirstStartLengthOnly_raw=@{$contigclustersFirstStartLengthOnly{$key2}}; my @contigclustersAllLastEndLengthOnly_raw=@{$contigclustersLastEndLengthOnly{$contigends[$i]{$key3}}}; my @contigclustersAllFirstStartLengthOnly=(); my @contigclustersAllLastEndLengthOnly=(); for my $val (0 ... $#contigclustersAllFirstStartLengthOnly_raw){ - print "val = $val\n" if $prinkter == 1; + # print "val = $val\n" if $prinkter == 1; if (defined $contigclustersAllFirstStartLengthOnly_raw[$val]){ push(@contigclustersAllFirstStartLengthOnly, $contigclustersAllFirstStartLengthOnly_raw[$val]) if $contigclustersAllFirstStartLengthOnly_raw[$val] =~ /[0-9]+/; } } - print "-----\n" if $prinkter == 1; + # print "-----\n" if $prinkter == 1; for my $val (0 ... $#contigclustersAllLastEndLengthOnly_raw){ - print "val = $val\n" if $prinkter == 1; + # print "val = $val\n" if $prinkter == 1; if (defined $contigclustersAllLastEndLengthOnly_raw[$val]){ push(@contigclustersAllLastEndLengthOnly, $contigclustersAllLastEndLengthOnly_raw[$val]) if $contigclustersAllLastEndLengthOnly_raw[$val] =~ /[0-9]+/; } } - print "our two arrays are: starts = <@contigclustersAllFirstStartLengthOnly> ......... and ends = <@contigclustersAllLastEndLengthOnly>\n" if $prinkter == 1; - print "the last cluster's end in that one is: ",smallest_number(@contigclustersAllFirstStartLengthOnly) + smallest_number(@contigclustersAllLastEndLengthOnly)," = ", smallest_number(@contigclustersAllFirstStartLengthOnly)," + ",smallest_number(@contigclustersAllLastEndLengthOnly),"\n" if $prinkter == 1; + # print "our two arrays are: starts = <@contigclustersAllFirstStartLengthOnly> ......... and ends = <@contigclustersAllLastEndLengthOnly>\n" if $prinkter == 1; + # print "the last cluster's end in that one is: ",smallest_number(@contigclustersAllFirstStartLengthOnly) + smallest_number(@contigclustersAllLastEndLengthOnly)," = ", smallest_number(@contigclustersAllFirstStartLengthOnly)," + ",smallest_number(@contigclustersAllLastEndLengthOnly),"\n" if $prinkter == 1; # if ($contigclustersFirstStartLengthOnly{$key2}[$i] + $contigclustersLastEndLengthOnly{$contigends[$i]{$key3}}[$i] < 50){ if (smallest_number(@contigclustersAllFirstStartLengthOnly) + smallest_number(@contigclustersAllLastEndLengthOnly) < $CLUSTER_DIST){ @@ -5119,7 +5165,7 @@ # print " clusteringpaths $key2 -> $contigends[$i]{$key3}\n"; $founkeys_enteredcount-- if exists $foundkeys{$key2}; $existing_removed++ if exists $foundkeys{$key2}; - print "$key2->",@{$contigclusters{$key2}},"->>$foundkeys{$key2}\n" if exists $foundkeys{$key2} && $prinkter == 1; +# print "$key2->",@{$contigclusters{$key2}},"->>$foundkeys{$key2}\n" if exists $foundkeys{$key2} && $prinkter == 1; delete $foundkeys{$key2} if exists $foundkeys{$key2}; $complete_transfered++; } @@ -5165,13 +5211,13 @@ my $pathed_count=0; foreach my $key2 (keys %foundkeys){ #print "x" x 60, "\n"; - print "x" if $dotcounter % 100 ==0; - print "\n" if $dotcounter % 5000 ==0; +# print "x" if $dotcounter % 100 ==0; +# print "\n" if $dotcounter % 5000 ==0; $founkeys_count++; my $key = $key2; - print "$key2 -> $clusteringpaths{$key2}\n" if $prinkter == 1; +# print "$key2 -> $clusteringpaths{$key2}\n" if $prinkter == 1; if ($clusteringpaths{$key} eq $key){ - print "printing hit the alignment block immediately... no path needed\n" if $prinkter == 1; +# print "printing hit the alignment block immediately... no path needed\n" if $prinkter == 1; $nopath_count++; delete $foundkeys{$key2}; print ORTH join ("\n",@{$contigclusters{$key2}}),"\n"; @@ -5180,43 +5226,43 @@ my @pool=(); my $key3=(); $pathed_count++; - print "going reverse... clusteringpathsRev, $key = $clusteringpathsRev{$key}\n" if exists $clusteringpathsRev{$key} && $prinkter == 1; - print "going reverse... clusteringpathsRev $key does not exist\n" if !exists $clusteringpathsRev{$key} && $prinkter == 1; +# print "going reverse... clusteringpathsRev, $key = $clusteringpathsRev{$key}\n" if exists $clusteringpathsRev{$key} && $prinkter == 1; +# print "going reverse... clusteringpathsRev $key does not exist\n" if !exists $clusteringpathsRev{$key} && $prinkter == 1; if ($clusteringpathsRev{$key} eq "0") { next; } else{ my $yek3 = $clusteringpathsRev{$key}; my $yek = $key; - print "caught in the middle of a path, now goin down from $yek to $yek3, which is $clusteringpathsRev{$key} \n" if $prinkter == 1; +# print "caught in the middle of a path, now goin down from $yek to $yek3, which is $clusteringpathsRev{$key} \n" if $prinkter == 1; while ($yek3 ne "0"){ - print "$yek->$yek3," if $prinkter == 1; +# print "$yek->$yek3," if $prinkter == 1; $yek = $yek3; $yek3 = $clusteringpathsRev{$yek}; } - print "\nfinally reached the end of path: $yek3, and the next in line is $yek, and its up-route is $clusteringpaths{$yek}\n" if $prinkter == 1; +# print "\nfinally reached the end of path: $yek3, and the next in line is $yek, and its up-route is $clusteringpaths{$yek}\n" if $prinkter == 1; $key3 = $clusteringpaths{$yek}; $key = $yek; } - print "now that we are at bottom of the path, lets start climbing up again\n" if $prinkter == 1; +# print "now that we are at bottom of the path, lets start climbing up again\n" if $prinkter == 1; while($key ne $key3){ - print "KEEY $key->$key3\n" if $prinkter == 1; - print "our contigcluster = @{$contigclusters{$key}}\n----------\n" if $prinkter == 1; +# print "KEEY $key->$key3\n" if $prinkter == 1; +# print "our contigcluster = @{$contigclusters{$key}}\n----------\n" if $prinkter == 1; if (scalar(@{$contigclusters{$key}}) > 0) {push @pool, @{$contigclusters{$key}}; print "now pool = @pool\n" if $prinkter == 1;} delete $foundkeys{$key3}; $key=$key3; $key3=$clusteringpaths{$key}; } - print "\nfinally, adding the first element of path: @{$contigclusters{$key}}\n AND printing the contents:\n" if $prinkter == 1; +# print "\nfinally, adding the first element of path: @{$contigclusters{$key}}\n AND printing the contents:\n" if $prinkter == 1; my @firstcontig= @{$contigclusters{$key}}; delete $foundkeys{$key2} if exists $foundkeys{$key2} ; delete $foundkeys{$key} if exists $foundkeys{$key}; unshift @pool, pop @firstcontig; - print join("\t",@pool),"\n" if $prinkter == 1; +# print join("\t",@pool),"\n" if $prinkter == 1; print ORTH join ("\n",@firstcontig),"\n" if scalar(@firstcontig) > 0; print ORTH join ("\t",@pool),"\n"; # join(); @@ -5224,7 +5270,7 @@ } #close (NORTH); - print "founkeys_entered =$founkeys_enteredcount, plain_transfered=$plain_transfered,existing_removed=$existing_removed,founkeys_count =$founkeys_count, nopath_count =$nopath_count, transfered = $transfered, complete_transfered = $complete_transfered, totalcount = $totalcount, pathed=$pathed_count\n" if $prinkter == 1; +# print "founkeys_entered =$founkeys_enteredcount, plain_transfered=$plain_transfered,existing_removed=$existing_removed,founkeys_count =$founkeys_count, nopath_count =$nopath_count, transfered = $transfered, complete_transfered = $complete_transfered, totalcount = $totalcount, pathed=$pathed_count\n" if $prinkter == 1; close (BO); close (ORTH); close (OUTP); --- a/tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml Wed Feb 09 16:49:43 2011 -0500 +++ b/tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml Thu Feb 10 10:33:08 2011 -0500 @@ -1,4 +1,4 @@ -<tool id="multispecies_orthologous_microsats" name="Extract orthologous microsatellites" version="1.0.0"> +<tool id="multispecies_orthologous_microsats" name="Extract orthologous microsatellites" version="1.0.1"><description> for multiple (>2) species alignments</description><command interpreter="perl"> multispecies_MicrosatDataGenerator_interrupted_GALAXY.pl Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Fix for MySQL index lengths in migration script 62. Thanks Leandro Hermida.
by Bitbucket 09 Feb '11

09 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/72cbd1ed1a81/ changeset: r5036:72cbd1ed1a81 user: natefoo date: 2011-02-09 22:49:43 summary: Fix for MySQL index lengths in migration script 62. Thanks Leandro Hermida. affected #: 1 file (1 byte) --- a/lib/galaxy/model/migrate/versions/0062_user_openid_table.py Wed Feb 09 16:46:30 2011 -0500 +++ b/lib/galaxy/model/migrate/versions/0062_user_openid_table.py Wed Feb 09 16:49:43 2011 -0500 @@ -40,7 +40,7 @@ ix_name = 'ix_galaxy_user_openid_openid' if migrate_engine.name == 'mysql': - i = "ALTER TABLE galaxy_user_openid ADD UNIQUE INDEX ( openid( 1000 ) )" + i = "ALTER TABLE galaxy_user_openid ADD UNIQUE INDEX ( openid( 255 ) )" db_session.execute( i ) else: i = Index( ix_name, UserOpenID_table.c.openid, unique=True ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: A fix for DRMs which can apparently cause a drmaa.InternalException in cases where the job is finished normally. If there are other conditions which raise this exception, failures may go undetected. The drmaa runner is not in active use by the development team, so please report problems with this change.
by Bitbucket 09 Feb '11

09 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/21cdfab7b813/ changeset: r5035:21cdfab7b813 user: natefoo date: 2011-02-09 22:46:30 summary: A fix for DRMs which can apparently cause a drmaa.InternalException in cases where the job is finished normally. If there are other conditions which raise this exception, failures may go undetected. The drmaa runner is not in active use by the development team, so please report problems with this change. affected #: 1 file (278 bytes) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: More comprehensive conflict resolution for eggs that are dependencies of other eggs, and eggs which conflict with system versions.
by Bitbucket 09 Feb '11

09 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/b69b84f67337/ changeset: r5034:b69b84f67337 user: natefoo date: 2011-02-09 22:31:43 summary: More comprehensive conflict resolution for eggs that are dependencies of other eggs, and eggs which conflict with system versions. affected #: 1 file (1.8 KB) --- a/lib/galaxy/eggs/__init__.py Wed Feb 09 16:29:50 2011 -0500 +++ b/lib/galaxy/eggs/__init__.py Wed Feb 09 16:31:43 2011 -0500 @@ -36,12 +36,13 @@ """ Contains information about locating and downloading eggs. """ - def __init__( self, name=None, version=None, tag=None, url=None, platform=None ): + def __init__( self, name=None, version=None, tag=None, url=None, platform=None, crate=None ): self.name = name self.version = version self.tag = tag self.url = url self.platform = platform + self.crate = crate self.distribution = None self.dir = None if self.name is not None and self.version is not None: @@ -145,37 +146,68 @@ log.debug( "Removed conflicting egg: %s" % doppelganger ) def resolve( self ): try: - return pkg_resources.working_set.resolve( ( self.distribution.as_requirement(), ), env, self.fetch ) + rval = [] + # resolve this egg and its dependencies + dists = pkg_resources.working_set.resolve( ( self.distribution.as_requirement(), ), env, self.fetch ) + for dist in dists: + # if any of the resolved dependencies should be managed eggs but are being pulled from the wrong path, fix them + if dist.project_name in self.crate.all_names and not os.path.realpath( dist.location ).startswith( os.path.realpath( self.dir ) ): + # TODO: like eggs.require(), this breaks requirement versioning + subdists = self.version_conflict( dist, dist.as_requirement() ) + if type( subdists ) == list: + rval.extend( subdists ) + else: + rval.append( subdists ) + else: + rval.append( dist ) + return rval except pkg_resources.DistributionNotFound, e: # If this statement is true, it means we do have the requested egg, # just not one (or more) of its deps. if e.args[0].project_name != self.distribution.project_name: - log.warning( "Warning: %s (a dependant egg of %s) cannot be fetched" % ( e.args[0].project_name, self.distribution.project_name ) ) + log.warning( "Warning: %s (a dependent egg of %s) cannot be fetched" % ( e.args[0].project_name, self.distribution.project_name ) ) return ( self.distribution, ) else: raise EggNotFetchable( self ) except pkg_resources.VersionConflict, e: # there's a conflicting egg on the path, remove it - dist = e.args[0] - # use the canonical path for comparisons - location = os.path.realpath( dist.location ) - for entry in pkg_resources.working_set.entries: - if os.path.realpath( entry ) == location: - pkg_resources.working_set.entries.remove( entry ) - break - else: - location = entry = None - del pkg_resources.working_set.by_key[dist.key] - if entry is not None: - pkg_resources.working_set.entry_keys[entry] = [] - if entry in sys.path: - sys.path.remove(entry) - r = pkg_resources.working_set.resolve( ( self.distribution.as_requirement(), ), env, self.fetch ) - if location is not None and not location.endswith( '.egg' ): - # re-add the path if it's a non-egg dir, in case more deps live there - pkg_resources.working_set.entries.append( location ) - sys.path.append( location ) - return r + return self.version_conflict( e.args[0], e.args[1] ) + def version_conflict( self, conflict_dist, conflict_req ): + # since this conflict may be for a dependent egg, find the correct egg from the crate + if conflict_dist.project_name == self.distribution.project_name: + egg = self + dist = egg.distribution + elif conflict_dist.project_name in self.crate.all_names: + egg = self.crate[conflict_dist.project_name] + dist = egg.distribution + else: + # should not happen, but just in case + egg = None + dist = conflict_dist + # use the canonical path to locate and remove the conflict from the working set + location = os.path.realpath( conflict_dist.location ) + for entry in pkg_resources.working_set.entries: + if os.path.realpath( entry ) == location: + pkg_resources.working_set.entries.remove( entry ) + break + else: + location = entry = None + del pkg_resources.working_set.by_key[conflict_dist.key] + # remove the conflict from sys.path + if entry is not None: + pkg_resources.working_set.entry_keys[entry] = [] + if entry in sys.path: + sys.path.remove(entry) + # if the conflict is a dpeendent egg, fetch that specific egg + if egg: + r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) + else: + r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env ) + # re-add the path if it's a non-egg dir, in case more deps live there + if location is not None and not location.endswith( '.egg' ): + pkg_resources.working_set.entries.append( location ) + sys.path.append( location ) + return r def require( self ): try: dists = self.resolve() @@ -215,7 +247,7 @@ platform = self.platform or '-'.join( ( py, pkg_resources.get_platform() ) ) else: platform = self.py_platform or py - egg = egg_class( name, version, tag, url, platform ) + egg = egg_class( name=name, version=version, tag=tag, url=url, platform=platform, crate=self ) self.eggs[name] = egg @property def config_missing( self ): @@ -331,7 +363,7 @@ return False def get_env(): - env = pkg_resources.Environment( platform=pkg_resources.get_platform() ) + env = pkg_resources.Environment( search_path='', platform=pkg_resources.get_platform() ) for dist in pkg_resources.find_distributions( os.path.join( galaxy_dir, 'eggs' ), False ): env.add( dist ) return env @@ -340,6 +372,8 @@ def require( req_str ): c = Crate() req = pkg_resources.Requirement.parse( req_str ) + # TODO: This breaks egg version requirements. Not currently a problem, but + # it could become one. try: return c[req.project_name].require() except KeyError: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Fixes for scrambling python-daemon and pysam.
by Bitbucket 09 Feb '11

09 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/ad054a328b74/ changeset: r5033:ad054a328b74 user: natefoo date: 2011-02-09 22:29:50 summary: Fixes for scrambling python-daemon and pysam. affected #: 3 files (67 bytes) --- a/dist-eggs.ini Wed Feb 09 16:18:56 2011 -0500 +++ b/dist-eggs.ini Wed Feb 09 16:29:50 2011 -0500 @@ -96,5 +96,6 @@ ; don't build these eggs on these platforms: [ignore] GeneTrack = py2.4 +python-daemon = py2.4 pysam = py2.4-solaris-2.8-sun4u_32-ucs2 py2.5-solaris-2.8-sun4u_32-ucs2 py2.6-solaris-2.8-sun4u_32-ucs2 py2.4-solaris-2.8-sun4u_64-ucs2 py2.5-solaris-2.8-sun4u_64-ucs2 py2.6-solaris-2.8-sun4u_64-ucs2 ctypes = py2.5-linux-i686-ucs2 py2.5-linux-i686-ucs4 py2.6-linux-i686-ucs2 py2.6-linux-i686-ucs4 py2.5-linux-x86_64-ucs2 py2.5-linux-x86_64-ucs4 py2.6-linux-x86_64-ucs2 py2.6-linux-x86_64-ucs4 py2.5-macosx-10.3-fat-ucs2 py2.6-macosx-10.3-fat-ucs2 py2.6-macosx-10.6-universal-ucs2 py2.5-solaris-2.10-i86pc_32-ucs2 py2.6-solaris-2.10-i86pc_32-ucs2 py2.5-solaris-2.10-i86pc_64-ucs2 py2.6-solaris-2.10-i86pc_64-ucs2 py2.5-solaris-2.8-sun4u_32-ucs2 py2.6-solaris-2.8-sun4u_32-ucs2 py2.5-solaris-2.8-sun4u_64-ucs2 py2.6-solaris-2.8-sun4u_64-ucs2 --- a/scripts/scramble/scripts/pysam-solaris.py Wed Feb 09 16:18:56 2011 -0500 +++ b/scripts/scramble/scripts/pysam-solaris.py Wed Feb 09 16:29:50 2011 -0500 @@ -24,6 +24,7 @@ cc = get_solaris_compiler() if cc == 'cc': os.environ['CFLAGS'] = '-xc99=all' + os.environ['LDFLAGS'] = '-lsocket -lnsl' # do it execfile( "setup.py", globals(), locals() ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Optimize the printed output of the 0074... migration script.
by Bitbucket 09 Feb '11

09 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/c366f4f232ea/ changeset: r5032:c366f4f232ea user: greg date: 2011-02-09 22:18:56 summary: Optimize the printed output of the 0074... migration script. affected #: 1 file (29 bytes) --- a/lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py Wed Feb 09 15:42:42 2011 -0500 +++ b/lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py Wed Feb 09 16:18:56 2011 -0500 @@ -48,10 +48,10 @@ cmd = "SELECT * FROM library_dataset WHERE deleted = %s;" % boolean_true() deleted_lds = db_session.execute( cmd ).fetchall() for row in deleted_lds: - print "Processing LibraryDataset id: ", int( row.id ) cmd = "SELECT * FROM library_dataset_dataset_association WHERE library_dataset_id = %d AND library_dataset_dataset_association.deleted = %s;" % ( int( row.id ), boolean_false() ) active_lddas = db_session.execute( cmd ).fetchall() if not active_lddas: + print "Updating purged column to True for LibraryDataset id : ", int( row.id ) cmd = "UPDATE library_dataset SET purged = %s WHERE id = %d;" % ( boolean_true(), int( row.id ) ) db_session.execute( cmd ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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