diff --git a/README.md b/README.md index c2270cf..06030b8 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ islandviewer-ui =============== -Web UI for Islandviewer +Web UI for Islandviewer. diff --git a/scripts/__init__.py b/scripts/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/scripts/mauve-wrapper.sh b/scripts/mauve-wrapper.sh new file mode 100644 index 0000000..cc9bac8 --- /dev/null +++ b/scripts/mauve-wrapper.sh @@ -0,0 +1,4 @@ +#!/bin/bash +#PBS -S /bin/bash + +/progressiveMauve --output=$1.xmfa --backbone-output=$2.backbone $3 $4 \ No newline at end of file diff --git a/scripts/mauvewrap.py b/scripts/mauvewrap.py new file mode 100644 index 0000000..775ed3a --- /dev/null +++ b/scripts/mauvewrap.py @@ -0,0 +1,85 @@ +import subprocess +import time +import shutil +import os +import xml.etree.ElementTree as ET + +#This can file can be moved to lib after testing +#These paths can be moved to the settings file after testing +MAUVE_PATH = "/data/Modules/iv-backend/islandviewer_dev/utils/mauve_2.4.0/linux-x64/progressiveMauve" +MAUVE_OUTPUT_PATH = "/data/Modules/iv-backend/islandviewer/pairwise_mauve" + +#Parameters = path to 2 genebank files +#Returns None +#Creates an output file at path outputfile and backbone file at path backbonefile +def runMauve(gbk1,gbk2,outputfile=None,outputbackbonefile=None, async=False): + if outputfile is None: + outputfile = MAUVE_OUTPUT_PATH+"/"+os.path.splitext(os.path.basename(gbk1))[0]+"-"+os.path.splitext(os.path.basename(gbk2))[0] + if outputbackbonefile is None: + outputbackbonefile = MAUVE_OUTPUT_PATH+"/"+os.path.splitext(os.path.basename(gbk1))[0]+"-"+os.path.splitext(os.path.basename(gbk2))[0] + + gbk1temppath = MAUVE_OUTPUT_PATH+"/"+os.path.basename(gbk1) + gbk2temppath = MAUVE_OUTPUT_PATH+"/"+os.path.basename(gbk2) + + shutil.copyfile(gbk1,gbk1temppath) + shutil.copyfile(gbk2,gbk2temppath) + + jobFile = outputfile+".pbs" + pbsFile = open(jobFile,"w+") + pbsFile.write("#!/bin/bash") + pbsFile.write("#PBS -S /bin/bash") + pbsFile.write(MAUVE_PATH+" --output="+outputfile+".xmfa --backbone-output=" + +outputbackbonefile+".backbone "+gbk1temppath+" "+gbk2temppath) + pbsFile.close() + sp = subprocess.Popen(["qsub", jobFile], cwd=MAUVE_PATH) + + # waits for job when using torque if async = False + if not async: + completeFlag = False + while not completeFlag: + qstatOutput = subprocess.Popen(["qstat", "-x"],stdout=subprocess.PIPE, cwd=MAUVE_PATH) + output = qstatOutput.communicate()[0] + tree = ET.fromstring(output) + matchfile = os.path.basename(jobFile) + for index in range(0,len(tree)): + currentFile = tree[index][1].text + if currentFile == matchfile: + status = tree[index][4].text + if status == 'C': + completeFlag = True + else: + if status != 'R': + completeFlag = True + print "Error has occured to submitted job (cluster)" + if not completeFlag: + time.sleep(60) + +#Given the paths of 2 genebank files, returns path of backbone file if it exists or None if it doesnt +def retrieveBackboneFile(gbk1,gbk2): + backbonepath = MAUVE_OUTPUT_PATH+"/"+os.path.splitext(os.path.basename(gbk1))[0]+"-"+os.path.splitext(os.path.basename(gbk2))[0]+".backbone" + if os.path.isfile(backbonepath): + return backbonepath + else: + return None + +#Wrapper for retrieving a backbone file. If it doesnt exist, this will call runMauve to create it. +def getMauveResults(gbk1,gbk2): + if retrieveBackboneFile(gbk1,gbk2) is None: + runMauve(gbk1,gbk2) + return retrieveBackboneFile(gbk1,gbk2) + + +##################### TESTS + +def testRunMauve(): + runMauve("/vagrant/islandviewer-ui/scripts/testFiles/AE009952.gbk","/vagrant/islandviewer-ui/scripts/testFiles/BX936398.gbk") + +def testRetrieveBackboneFiles(): + print(retrieveBackboneFile("/vagrant/islandviewer-ui/scripts/testFiles/AE009952.gbk","/vagrant/islandviewer-ui/scripts/testFiles/BX936398.gbk")) + +def testList(): + #testRunMauve() + #testRetrieveBackboneFiles() + print getMauveResults("/vagrant/islandviewer-ui/scripts/testFiles/AE009952.gbk","/vagrant/islandviewer-ui/scripts/testFiles/BX936398.gbk") + +#testList() \ No newline at end of file diff --git a/static/css/islandviewer.css b/static/css/islandviewer.css index 998747e..5edff9c 100644 --- a/static/css/islandviewer.css +++ b/static/css/islandviewer.css @@ -93,6 +93,10 @@ body { padding: 10px; } +input#gene_search_input{ + width:100%; +} + .chkLabel input { float: left; margin-top:0.5em;} .chkLabel span { display: block; margin-left: 1.5em;} @@ -209,6 +213,9 @@ div.outline { color: #1F1A80; letter-spacing:0.1em; line-height:26px; + display: inline-block; + white-space: normal; + width: 500px; } .linearLabel { @@ -347,6 +354,10 @@ input[type=file] { border: 1px solid #808080; } +#outer_circular{ + white-space: nowrap; +} + /* Section for GI tables */ .gitable_fullwidth { max-width: 100%; @@ -636,4 +647,9 @@ input[type=file] { transform: rotate(360deg); } } + +.linearchart { + width: 100%; +} + /* END Spinner for loading ranking page*/ diff --git a/static/examples/pseudomonas.backbone b/static/examples/pseudomonas.backbone new file mode 100644 index 0000000..d6e1221 --- /dev/null +++ b/static/examples/pseudomonas.backbone @@ -0,0 +1,686 @@ +seq0_leftend seq0_rightend seq1_leftend seq1_rightend +1 16876 1 16877 +16880 52931 16904 52951 +52961 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3406757 +0 0 3413598 3413636 +0 0 3484858 3485025 +0 0 3511653 3515887 +0 0 3516775 3516848 +0 0 3516952 3520877 +0 0 3522321 3522412 +0 0 3543841 3544128 +0 0 3544176 3545328 +0 0 3555731 3560405 +0 0 3572704 3575154 +0 0 3590881 3595796 +0 0 3615177 3616811 +0 0 3831839 3840947 +0 0 3848627 3848650 +0 0 3894198 3894234 +0 0 3933007 3933036 +0 0 3972146 3972165 +0 0 3974530 3975628 +0 0 3999657 3999792 +0 0 4010973 4011006 +0 0 4127950 4130612 +0 0 4133008 4135141 +0 0 4138368 4154760 +0 0 4160542 4160582 +0 0 4286574 4286689 +0 0 4345135 4355802 +0 0 4399212 4399468 +0 0 4399531 4399596 +0 0 4399641 4401098 +0 0 4401142 4401253 +0 0 4401409 4401444 +0 0 4401548 4401769 +0 0 4402535 4405653 +0 0 4406263 4407274 +0 0 4463326 4463621 +0 0 4464772 4464855 +0 0 4465240 4465309 +0 0 4465715 4466335 +0 0 4466995 4467231 +0 0 4468060 4475139 +0 0 4580323 4589261 +0 0 4615402 4615423 +0 0 4656780 4656815 +0 0 4750087 4755876 +0 0 4757860 4757950 +0 0 4760866 4761001 +0 0 4761175 4761246 +0 0 4793697 4794249 +0 0 4860227 4895127 +0 0 4902082 4902108 +0 0 4919806 4919952 +0 0 4920322 4920352 +0 0 4920840 4920955 +0 0 4921048 4921318 +0 0 4921535 4921614 +0 0 4923485 4923569 +0 0 4924163 4926797 +0 0 4930901 4931260 +0 0 4952364 4957703 +0 0 5131709 5131745 +0 0 5214358 5214488 +0 0 5232807 5233933 +0 0 5234124 5234177 +0 0 5251435 5251459 +0 0 5253764 5253822 +0 0 5257428 5257448 +0 0 5260129 5260164 +0 0 5260994 5261060 +0 0 5264243 5264277 +0 0 5264505 5264826 +0 0 5266813 5267102 +0 0 5267505 5268084 +0 0 5270120 5270687 +0 0 5271429 5271474 +0 0 5274596 5274654 +0 0 5274866 5277615 +0 0 5289366 5289587 +0 0 5293797 5294016 +0 0 5301073 5303963 +0 0 5312671 5312785 +0 0 5312817 5328353 +0 0 5346006 5346091 +0 0 5347414 5355584 +0 0 5357546 5359391 +0 0 5369975 5370033 +0 0 5370209 5370398 +0 0 5370556 5370595 +0 0 5372012 5377452 +0 0 5459651 5459728 +0 0 5536247 5541567 +0 0 5633184 5633288 +0 0 5657659 5658317 +0 0 5725735 5725949 +0 0 5739731 5740525 +0 0 5883641 5883678 +0 0 5996029 5996910 +0 0 5997038 5998796 +0 0 6097967 6098007 +0 0 6198205 6204566 +0 0 6312733 6318084 +0 0 6460858 6461077 +0 0 6461174 6461402 +0 0 6482650 6482720 +0 0 6497907 6497949 +0 0 6514741 6515047 diff --git a/static/js/alignervis.js b/static/js/alignervis.js new file mode 100644 index 0000000..d9217b3 --- /dev/null +++ b/static/js/alignervis.js @@ -0,0 +1,267 @@ +//Notes: seems appropriate to move Multivis.sequences to Backbone + +function MultiVis(targetNode){ + var self = this; + const SEQUENCEHEIGHT = 150; + const CONTAINERWIDTH = 1115; + // const NUMBERAXISTICKS = 5; BROKEN FOR CURRENT IMPLEMENTATION + + this.container = d3.select(targetNode); + this.backbone = new Backbone(); + this.sequences = this.backbone.getSequences(); + + this.getSequence = function(index){ + return self.sequences[index]; + }; + + this.getLargestSequenceSize = function(){ + var largestSize=0; + for (var i = 0; ilargestSize){ + largestSize = this.sequences[i].getSequenceSize(); + } + } + return largestSize; + }; + + this.containerWidth = function() { + if (CONTAINERWIDTH != null){ + return CONTAINERWIDTH; + } + else { + return this.container.node().getBoundingClientRect().width; + } + }; + + this.containerHeight = function() { + return this.sequences.length*SEQUENCEHEIGHT-100;// The -100 fixes padding issues on islandviewer site, fix this later if required; + }; + + this.updateSequenceVisualization= function(sequenceIndex, newstart, newend){ + try { + self.getSequence(sequenceIndex).updateScale(newstart, newend, CONTAINERWIDTH); + self.transition(); + }catch(e){ + //Chart may not have been initialized yet (call parseandrender?) + } + }; + + //Readjusts the graph for updated sequence domains, (improve later, currently just re-renders graph) + this.transition = function(){ + this.container.select("svg").remove(); + this.render(); + }; + + this.render = function (){ + this.container.select("svg").remove(); + var scale = d3.scale.linear().domain([0,this.getLargestSequenceSize()]).range([0,this.containerWidth()]); + + //Add the SVG + var svg = this.container.append("svg") + .attr("width",this.containerWidth()) + .attr("height",this.containerHeight()); + + //Draw Homologous Region Lines + var lines = []; + + for (var i=0; i largestBase[k]){ + largestBase[k] = Number(data[row]["seq"+k+"_rightend"]); + } + } + + //Dont Load "Matches" that do not contain a homologous region + if (data[row]["seq" + choicelist[choice][0] + "_rightend"] == 0 || data[row]["seq" + choicelist[choice][1] + "_rightend"] == 0){ + continue; + } + + backbonereference.addHomologousRegion( choicelist[choice][0], choicelist[choice][1], + data[row]["seq" + choicelist[choice][0] + "_leftend"], + data[row]["seq" + choicelist[choice][0] + "_rightend"], + data[row]["seq" + choicelist[choice][1] + "_leftend"], + data[row]["seq" + choicelist[choice][1] + "_rightend"]); + } + } + + for (var i=0; i + + + + Title + + + + + + +
+ +
+ + + \ No newline at end of file diff --git a/static/js/islandviewer.js b/static/js/islandviewer.js index fc5a2cd..b50ea57 100644 --- a/static/js/islandviewer.js +++ b/static/js/islandviewer.js @@ -9,27 +9,44 @@ function Islandviewer(aid, ext_id, genomesize, genomename, trackdata) { this.startBP = 0; this.endBP = genomesize; + this.linearplot = null; + this.comparisoncontainer = null; } +Islandviewer.prototype.addComparison = function(comparisonfunction){ + this.comparisoncontainer = comparisonfunction; + +}; + Islandviewer.prototype.addCircularPlot = function(layout) { this.circularplot = new circularTrack(layout, this.trackdata); $(layout.container).addClass('plot_' + this.ext_id.replace('.', '')); return this.circularplot; -} +}; Islandviewer.prototype.addLinearPlot = function(layout) { this.linearplot = new genomeTrack(layout, this.trackdata); + try { + if (this.comparisoncontainer != undefined) { + this.linearplot.setComparisonContainer(this.comparisoncontainer); + } + } catch (e){ + + } + + console.log(this.linearplot); return this.linearplot; +}; + +Islandviewer.prototype.setComparisonContainer = function(comparisonfunction){ + this.comparisoncontainer = comparisonfunction; + this.linearplot.setComparisonContainer(this.comparisoncontainer) } Islandviewer.prototype.onclick = function(trackname, d, plotid, skip_half_range) { -// console.log("Got a callback " + d); -// console.log(trackname); -// console.log(d); -// console.log(plotid); if(plotid == 'circularchartlinear' || plotid == 'secondchartlinear') { @@ -136,10 +153,6 @@ Islandviewer.prototype.focus = function(startbp, endbp, params) { } Islandviewer.prototype.mouseover = function(trackname, d, plotid) { -// console.log("Got a callback " + d); -// console.log(trackname); -// console.log(d); -// console.log(plotid); if(plotid == 'circularchartlinear' || plotid == 'secondchartlinear' ) { if(trackname == 'circularGenes') { diff --git a/static/js/linearbrush.js b/static/js/linearbrush.js index db905a1..6b2a1a9 100644 --- a/static/js/linearbrush.js +++ b/static/js/linearbrush.js @@ -3,7 +3,7 @@ contextWidth = 440 - contextMargin.left - contextMargin.right, contextHeight = 100 - contextMargin.top - contextMargin.bottom; function linearBrush(layout, callbackObj) { - this.layout; + this.layout = layout; this.callbackObj = callbackObj; this.brushContainer = d3.select(layout.container) @@ -50,7 +50,7 @@ function linearBrush(layout, callbackObj) { function brushUpdate(b) { var minExtent = brush.extent()[0]; var maxExtent = brush.extent()[1]; - // console.log(minExtent, maxExtent); + //console.log(minExtent, maxExtent); callbackObj.update(minExtent, maxExtent); } diff --git a/static/js/linearplot.js b/static/js/linearplot.js index 253a6af..fa40c2c 100644 --- a/static/js/linearplot.js +++ b/static/js/linearplot.js @@ -10,23 +10,25 @@ var linearTrackDefaults = { }; function genomeTrack(layout,tracks) { + console.log(layout); this.tracks = tracks; this.layout = layout; this.numTracks = this.countTracks(); + this.comparisonContainerCallback = null; if('undefined' !== typeof layout) { - // Copy over any defaults not passed in - // by the user - for(var i in linearTrackDefaults) { - if('undefined' == typeof layout[i]) { - this.layout[i] = linearTrackDefaults[i]; - } - } + // Copy over any defaults not passed in + // by the user + for(var i in linearTrackDefaults) { + if('undefined' == typeof layout[i]) { + this.layout[i] = linearTrackDefaults[i]; + } + } } if('undefined' == typeof layout.plotid) { - this.layout.plotid = layout.container.slice(1); + this.layout.plotid = layout.container.slice(1); } this.layout.containerid = layout.container.slice(1); @@ -41,14 +43,14 @@ function genomeTrack(layout,tracks) { this.itemRects = []; this.x = d3.scale.linear() - .domain([0, layout.genomesize]) - .range([0,this.layout.width_without_margins]); + .domain([0, layout.genomesize]) + .range([0,this.layout.width_without_margins]); this.x1 = d3.scale.linear() - .range([0,this.layout.width_without_margins]) + .range([0,this.layout.width_without_margins]) .domain([0, layout.genomesize]); this.y1 = d3.scale.linear() - .domain([0,this.numTracks]) - .range([0,(this.layout.height_without_axis-this.layout.bottom_margin)]); + .domain([0,this.numTracks]) + .range([0,(this.layout.height_without_axis-this.layout.bottom_margin)]); // We need x1 and y1 in the initialization's scope too // to deal with passing it in to make the lollipops @@ -77,10 +79,8 @@ function genomeTrack(layout,tracks) { .attr("id", "trackClip_" + this.layout.containerid) .append("rect") .attr("width", this.layout.width_without_margins) - // .attr("width", this.layout.width_without_margins + this.layout.right_margin) .attr("height", this.layout.height) .attr("transform", "translate(0,0)"); - // .attr("transform", "translate(" + this.layout.left_margin + ",0)"); this.drawFeatures(); @@ -993,7 +993,7 @@ genomeTrack.prototype.displayAxis = function() { } genomeTrack.prototype.update = function(startbp, endbp, params) { - // console.log(startbp, endbp); + //console.log(startbp, endbp); this.visStart = startbp; this.visEnd = endbp; @@ -1004,7 +1004,7 @@ genomeTrack.prototype.displayAxis = function() { } genomeTrack.prototype.update_finished = function(startbp, endbp, params) { - // console.log("Thank you, got: " + startbp, endbp); + //console.log("Thank you, got: " + startbp, endbp); } @@ -1047,6 +1047,7 @@ genomeTrack.prototype.dragresize = function(d) { } genomeTrack.prototype.redraw = function() { + this.comparisonRedrawer(); for(var i = 0; i < this.tracks.length; i++) { @@ -1077,8 +1078,18 @@ genomeTrack.prototype.redraw = function() { } this.axisContainer.select(".xaxislinear").call(this.xAxis); +}; -} +genomeTrack.prototype.setComparisonContainer = function(comparisoncontainerfunction){ + this.comparisonContainerCallback = comparisoncontainerfunction; +}; + +genomeTrack.prototype.comparisonRedrawer = function(){ + var sequenceid = this.layout.id; + if (this.comparisonContainerCallback != undefined){ + this.comparisonContainerCallback(sequenceid, this.visStart, this.visEnd); + } +}; genomeTrack.prototype.rescale = function() { var cfg = this.layout; diff --git a/templates/about.html b/templates/about.html index 6cc5876..c41e615 100644 --- a/templates/about.html +++ b/templates/about.html @@ -4,14 +4,17 @@ {% block sidebar %}

Definitions

-

Genomic Islands - large genomic regions (typically > 8kb), that are thought to have horizontal origins. These regions can often contain genes that are related to antibiotic resistance or virulence.

- -

Sequence Composition GI Prediction Methods - bacterial genomes tend to naturally have differences in sequence composition such as GC% and codon bias. Therefore, a region within a genome that has abnormal sequence composition could indicate that it originated from another genome. Various tools (incl. SIGI-HMM and IslandPath-DIMOB) look for regions with abnormal sequence composition.

- -

Comparative Genomic GI Prediction Methods - genomic regions that are not present within related strains suggest that the region was horizontally transferred. IslandPick is a method that automatically selects comparison genomes that are within a proper evolutionary distance and identifies regions that are unique to only a single genome.

- -

Mobility Genes - are genes related to the movement of mobile genetic elements (incl. genomic islands), such as transposases and integrases.

- +

Genomic Islands - large genomic regions (typically > 8kb), that are thought to have horizontal origins. These regions can often contain genes that are related to antibiotic resistance or virulence.

+ +

Sequence Composition GI Prediction Methods - bacterial genomes tend to naturally have differences in sequence composition such as GC% and codon bias. Therefore, a region within a genome that has abnormal sequence composition could indicate that it originated from another genome. Various tools (incl. SIGI-HMM and IslandPath-DIMOB) look for regions with abnormal sequence composition.

+ +

Comparative Genomic GI Prediction Methods - genomic regions that are not present within related strains suggest that the region was horizontally transferred. IslandPick is a method that automatically selects comparison genomes that are within a proper evolutionary distance and identifies regions that are unique to only a single genome.

+ +

Mobility Genes - are genes related to the movement of mobile genetic elements (incl. genomic islands), such as transposases and integrases.

+ +  
+ + {% include "citation.html" %} {% endblock sidebar %} {% block content %} @@ -32,7 +35,7 @@

IslandViewer

-

This web site was developed so that researchers could easily view and download genomic islands for all published sequenced bacterial and archaeal genomes that have been predicted using the the currently most accurate GI prediction methods. Users can also upload their own unpublished genomes for analysis. The source code and entire GI data sets are available for download and acknowledgment information is available for those who use our resources . Please contact us with any questions or comments. Note, this is IslandViewer 3, the older IslandViewer 2 is still available for any old analysis needs.

+

This web site was developed so that researchers could easily view and download genomic islands for all published sequenced bacterial and archaeal genomes that have been predicted using the the currently most accurate GI prediction methods. Users can also upload their own unpublished genomes for analysis. The source code and entire GI data sets are available for download and acknowledgment information is available for those who use our resources. This software and website is developed and maintained by the Brinkman lab at Simon Fraser University, Canada. Please contact us with any questions or comments. Note, this is IslandViewer 3, the older IslandViewer 2 is still available for any old analysis needs.

IslandPick

diff --git a/templates/acknowledgements.html b/templates/acknowledgements.html index 9854ae8..169a080 100644 --- a/templates/acknowledgements.html +++ b/templates/acknowledgements.html @@ -1,28 +1,34 @@ {% extends "base.html" %} {% load static %} +{% block sidebar %} +

IslandViewer software is being developed by the Brinkman lab at Simon Fraser University, Canada

+{% endblock sidebar %} + + {% block content %}

Acknowledgements

-

We would appreciate that anyone who uses IslandViewer to cite:

+

We would appreciate anyone who uses IslandViewer to cite:

Dhillon, B.K., Laird, M.R., Shay, J.A., Winsor, G.L., Lo, R., Nizam, F., Pereira, S.K., Waglechner, N., McArthur A.G., Langille, M.G.I., and Brinkman, F.S.L. (2015). "IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis", Nucleic Acids Research, 43 (W1): W104-W108. doi: 10.1093/nar/gkv401
+ and note these earlier papers: -
- Dhillon, B.K., Chiu, T.A., Laird, M.R., Langille, M.G.I., and Brinkman, F.S.L. (2013). “IslandViewer update: improved genomic island discovery and visualization“, Nucleic Acids Research, 41(Web server issue):W129-132. PMID: 23677610 -
-
- Langille, M.G.I. and F.S.L. Brinkman (2009). “IslandViewer: an integrated interface for computational identification and visualization of genomic islands”, Bioinformatics, Jan. 16 (EPub). PMID: 19151094 -
+
+ Dhillon, B.K., Chiu, T.A., Laird, M.R., Langille, M.G.I., and Brinkman, F.S.L. (2013). “IslandViewer update: improved genomic island discovery and visualization“, Nucleic Acids Research, 41(Web server issue):W129-132. doi: 10.1093/nar/gkt394 +
+  
+ Langille, M.G.I. and Brinkman, F.S.L. (2009). “IslandViewer: an integrated interface for computational identification and visualization of genomic islands”, Bioinformatics, (2009) 25 (5): 664-665. doi: 10.1093/bioinformatics/btp030 +

In addition, depending on the resources used, we would encourage the acknowledgement of one or more of the following resources:

  • SIGI-HMM (Waack et al., 2006)
    • -
  • IslandPath-DIMOB (Langille et al., 2008)
    • +
  • IslandPath-DIMOB (Hsiao et al., 2003, Hsiao et al., 2005 and Langille et al., 2008)
  • IslandPick (Langille et al., 2008)
  • Mauve (Darling et al. 2010; Rissman et al., 2009)
  • Virulence Factor Database - VFDB - (Chen et al., 2012)
    • diff --git a/templates/circularplot.js b/templates/circularplot.js index fa14ca3..a26981e 100644 --- a/templates/circularplot.js +++ b/templates/circularplot.js @@ -8,6 +8,7 @@ var {{ varName|default:"circular" }}data = [ visible: false, showLabels: true, showTooltip: true, + showTooltip: true, //skipLinear: true, linear_skipInit: true, {% if ext_id %}ext_id: '{{ext_id}}', @@ -140,10 +141,14 @@ var {{ varName|default:"circular" }}_aid = "{{ aid }}"; {% comment %}Skip the entire code section if we're just pulling in another plot's data{% endcomment %} {% if not skip_initialize %} -var islandviewerObj = new Islandviewer('{{ aid }}', '{{ext_id}}', {{ genomesize|default:"0" }}, "{{ genomename }}", {{ plotName|default:"circular" }}data); -// {{ genomename|pprint }} +window.container = new MultiVis("#linearchartcomparisons"); +window.islandviewerObj = new Islandviewer('{{ aid }}', '{{ext_id}}', {{ genomesize|default:"0" }}, "{{ genomename }}", {{ plotName|default:"circular" }}data); +window.islandviewerObj.addComparison(window.container.updateSequenceVisualization); + update_legend(); + + var {{ plotName|default:"circular" }}layout = {genomesize: {{ genomesize }}, container: "{{ container }}", h: 500, w: 500, ExtraWidthX: 55, TranslateX: 25, ExtraWidthY: 40, TranslateY: 20, movecursor: true, dblclick: '{{ varName|default:'' }}islandviewerObj' }; var {{ varName|default:"circular" }}containerid = "{{ container }}".slice(1); @@ -153,7 +158,9 @@ var {{ plotName|default:"circular" }}TrackObj = islandviewerObj.addCircularPlot( $('#loadingimg').remove(); -var {{ plotName|default:"circular" }}Linearlayout = {genomesize: {{ genomesize }}, container: "{{ container }}linear", width: 600, height: 135, bottom_margin:0, initStart:0, initEnd: Math.min(1000, {{ genomesize }})}; +var linearcontainerwidth = 1115; + +var {{ plotName|default:"circular" }}Linearlayout = {id: 0,genomesize: {{ genomesize }}, container: "{{ container }}linear", width: linearcontainerwidth, height: 135, bottom_margin:0, initStart:0, initEnd: Math.min(1000, {{ genomesize }})}; //var {{ plotName|default:"circular" }}LinearTrack = new genomeTrack({{ plotName|default:"circular" }}Linearlayout, {{ plotName|default:"circular" }}data); var {{ plotName|default:"circular" }}LinearTrack = islandviewerObj.addLinearPlot({{ plotName|default:"circular" }}Linearlayout); @@ -172,12 +179,6 @@ $('#gene_dialog').dialog( { position: { my: "left top", at: "right top", of: "{{ } } ); -//$('#genome_selector_dialog').dialog( { position: { my: "center", at: "center", of: window }, -// height: 300, width: 600, -// title: "Select a genome", -// autoOpen: true -// } ); - function updateStrand(cb, strand) { var track = ''; @@ -215,7 +216,6 @@ function updateStrand(cb, strand) { } } -//var virulenceMappings = { 'VFDB': ['VFDB', 'Victors', 'Patric_VF'], var virulenceMappings = { 'VFDB': ['VFDB'], 'ARDB': ['ARDB', 'CARD'], 'BLAST': ['BLAST'], @@ -226,13 +226,8 @@ var virulenceMappings = { 'VFDB': ['VFDB'], function updateVirulence(cb, vir) { var vir_factor = vir; - // var vir_factors = virulenceMappings[vir]; - // for(var x = 0; x < vir_factors.length; x++) { - // vir_factor = vir_factors[x]; -// console.log(vir_factor); if(cb.checked) { - // console.log("showing: " + vir_factor); {{ plotName|default:"circular" }}TrackObj.showGlyphTrackType("{{ plotName|default:"circular" }}Virulence", vir_factor); if('undefined' !== typeof window.secondTrackObj) { window.secondTrackObj.showGlyphTrackType("{{ plotName|default:"circular" }}Virulence", vir_factor); @@ -282,7 +277,6 @@ window.onload = function() { var half_range = (item.end - item.start)/2; {{ plotName|default:"circular" }}LinearTrack.update(Math.max(0,(item.start-half_range)), Math.min({{ genomesize }}, (item.end+half_range))); -// {{ plotName|default:"circular" }}LinearTrack.update(2840000,2905000); {{ plotName|default:"circular" }}TrackObj.moveBrushbyBP(Math.max(0,(item.start-half_range)), Math.min({{ genomesize }}, (item.end+half_range))); @@ -294,16 +288,13 @@ window.onload = function() { } } - $("#second_genome_select").chosen({width: "525px"}); + $("#second_genome_select").chosen({width: "100%"}); initialize_gene_search(); if('undefined' !== typeof reloadStr) { - // console.log(reloadStr); reload(reloadStr); } - // reload(); -// load_second(); {% if contig_controls %} $('#contigcontrols').show(); @@ -318,7 +309,7 @@ function show_gene_search() { return; } - $('#show_gene_search').html("Hide search"); + $('#show_gene_search').html("Hide Search"); $('#gene_search_dialog').slideToggle('fast'); $("#gene_search_input").focus(); @@ -421,7 +412,6 @@ function serialize() { if('undefined' !== typeof window.secondislandviewerObj) { params['s'] = window.secondislandviewerObj.serialize(); - // params['s']['id'] = window.secondislandviewerObj.aid; } if($('#gene_dialog').dialog( "isOpen" ) === false) { @@ -430,7 +420,6 @@ function serialize() { params['d'] = {v: true}; var o = $('#gene_dialog').dialog( "open" ).offset(); - // params['d']['p'] = $('#gene_dialog').dialog('option', 'position'); params['d']['t'] = o.top; params['d']['l'] = o.left; @@ -440,10 +429,6 @@ function serialize() { uri = encodeURIComponent(JSON.stringify(params)); - // decoded = decodeURIComponent(uri); - - // console.log(decoded); - url = insertParam('load', uri); console.log(url); @@ -477,7 +462,6 @@ function insertParam(key, value) if(i<0) {kvp[kvp.length] = [key,value].join('=');} //this will reload the page, it's likely better to store this until finished - // document.location.search = kvp.join('&'); return document.location.href + '?' + kvp.join('&'); } @@ -489,7 +473,6 @@ function reload(paramsStr) { } catch(err) { alert("Error decoding url."); } - // console.log(params); if('undefined' !== typeof params['m']) { islandviewerObj.reload(params['m']); @@ -516,8 +499,8 @@ function reload(paramsStr) { } if('undefined' !== typeof params['s'] && 'undefined' !== typeof params['s']['id']) { - obj = load_second(params['s']['id'], params['s']); - // obj.reload(params['s']); + obj = load_second(params['s']['id'], params['s']); + // islandviewerObj.addComparison(window.container.updateSequenceVisualization); } } @@ -567,6 +550,10 @@ function show_genome_dialog() { }); } +function load_second_helper(aidParam, reloadParams){ + $("#linearchartcomparisons").toggle(); + var secondplot = load_second(aidParam,reloadParams); +} function load_second(aidParam, reloadParams) { aid = $("#second_genome_select").val(); @@ -575,8 +562,6 @@ function load_second(aidParam, reloadParams) { aid = aidParam; } -// console.log("loading " + aid); - if($('#genome_selector_dialog').is(":visible")) { $('#genome_selector_dialog').slideToggle(); } @@ -588,20 +573,22 @@ function load_second(aidParam, reloadParams) { var url = "{% url 'circularplotjs' '9999' %}".replace("9999", aid); url += "?skipinit=true&varname=second"; -// var url = "/islandviewer/plot/553?skipinit=true&varname=second"; - -// console.log(url); $("#loadingspinner").show("fast"); - $.getScript( url, function() { -// console.log("loaded"); -// console.log(second_genomesize); + + $.ajax({url:url, + type: "GET", + async: false, + cahce: false,}); window.secondislandviewerObj = new Islandviewer(aid, second_extid, second_genomesize, second_genomename, seconddata); - $('#second_genome_title').html(second_genomename); - // We can update hte legend here because it only depends on the dataset + container.backbone.parseAndRenderBackbone("getMauve/?firstgenomeextid="+islandviewerObj.ext_id+"&secondgenomeextid="+window.secondislandviewerObj.ext_id,container); + $("#linearchartcomparisons").toggle(); + + $('#second_genome_title').html(second_genomename); + // We can update the legend here because it only depends on the dataset update_legend(); // Update the tracks if any are turned off @@ -612,8 +599,11 @@ function load_second(aidParam, reloadParams) { window.secondTrackObj = secondislandviewerObj.addCircularPlot(secondlayout); $('#rightplot').draggable({ handle: ".move_rightplot" }); - var secondLinearlayout = {genomesize: second_genomesize, container: "#secondchartlinear", width: 600, height: 135, bottom_margin:0, plotid: 'circularchartlinear'}; + var secondLinearlayout = {id:1,genomesize: second_genomesize, container: "#secondchartlinear", width: linearcontainerwidth, height: 135, bottom_margin:0, plotid: 'circularchartlinear'}; // var secondLinearTrack = new genomeTrack(secondLinearlayout, seconddata); + + secondislandviewerObj.addComparison(window.container.updateSequenceVisualization); + window.secondLinearTrack = secondislandviewerObj.addLinearPlot(secondLinearlayout); secondTrackObj.attachBrush(secondLinearTrack); @@ -626,7 +616,9 @@ function load_second(aidParam, reloadParams) { for(var i=0; i < seconddata.length; i++) { if(seconddata[i].trackName == "{{ plotName|default:"circular" }}Integrated") { if(seconddata[i].items.length > 0) { - item = seconddata[i].items[0]; + item = seconddata[i].items[0];// console.log("loaded"); +// console.log(second_genomesize); + } var half_range = (item.end - item.start)/2; @@ -662,18 +654,19 @@ function load_second(aidParam, reloadParams) { $('#linearname').html({{ varName|default:"circular" }}_genomename); $('#secondlinearname').html(second_genomename); }); - +/* }).done(function() { if('undefined' !== typeof reloadParams) { window.secondislandviewerObj.reload(reloadParams); - } + }// console.log("loaded"); +// console.log(second_genomesize); +*/ $("#loadingspinner").hide("fast"); - }); // end getScript() - +// }); // end getScript()*/ return window.secondislandviewerObj; } @@ -721,7 +714,6 @@ function update_legend() { methods = secondmethods; } -//console.log(methods); // Now update the legend var allmethods = ['circularIntegrated', 'circularIslandpick', 'circularSigi', 'circularDimob', 'PAG', 'VFDB', 'ARDB', 'CARD', 'RGI', 'Victors', 'PATRIC_VF', 'BLAST']; // First disable all checkboxes and say nothing is run @@ -762,7 +754,7 @@ function feature_tour() { } intro.onexit(function() { if(dialog_was_open === false) { - $('#gene_dialog').dialog( "close" ); + $('#gene_dialog').dialog( "close timestamp on the file will change. When Apache sees the file has been updated, it will restart your Django application for you.") } hide_download(); // $('#download_dialog').addClass("hidden"); diff --git a/templates/citation.html b/templates/citation.html new file mode 100644 index 0000000..d246887 --- /dev/null +++ b/templates/citation.html @@ -0,0 +1,2 @@ + +
    If you use IslandViewer for your research, please cite the most recent publication. Thank You!
    Dhillon, B.K. et al. 2015.
    "IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis"
    Nucleic Acids Research, 43 (W1): W104-W108.
    doi: 10.1093/nar/gkv401
    diff --git a/templates/download.html b/templates/download.html index eb9fdfb..fcf475e 100644 --- a/templates/download.html +++ b/templates/download.html @@ -2,7 +2,7 @@ {% load static %} {% block sidebar %} -

    We would appreciate researchers acknowledge IslandViewer and any datasets that they have used.

    +

    We would appreciate researchers acknowledge IslandViewer and any datasets that they have used.

    {% endblock sidebar %} {% block content %} @@ -27,13 +27,13 @@

    Source Code

    -

    Please note that the following three methods are integrated into IslandViewer.

    +

    Please note that the following three methods are integrated into IslandViewer.

    -

    IslandPick is currently very dependent on an in-house MySQL database of all published genomes, and is optimized for use on our computer cluster. Although it would require a significant amount of effort for a casual user to install, we still believe in open access to our software. Therefore, those researchers with sophisticated bioinformatics backgrounds are welcome to view and use our source code, which is available under a GPL license here.

    +

    IslandPick is currently very dependent on an in-house MySQL database of all published genomes, and is optimized for use on our computer cluster. Although it would require a significant amount of effort for a casual user to install, we still believe in open access to our software. Therefore, those researchers with sophisticated bioinformatics backgrounds are welcome to view and use our source code, which is available under a GPL license here.

    IslandPath-DIMOB source code is available under a GPL license here. This code has been tested only on linux and requires that Perl, BioPerl, and HMMER be installed on the user's computer.

    -

    SIGI-HMM is available for download here.

    +

    SIGI-HMM is available for download here.

    We would encourage users to contact us with any special requests or concerns.

    diff --git a/templates/faq.html b/templates/faq.html index 65a8111..dd35afe 100644 --- a/templates/faq.html +++ b/templates/faq.html @@ -2,7 +2,9 @@ {% load static %} {% block sidebar %} -

    If you need further assistance, please feel free to email us at islandpick-mail@sfu.ca with your enquiries. Thank you.

    +

    If you need further assistance, please feel free to email us at islandpick-mail@sfu.ca with your enquiries. Thank you.

    +  
    + {% include "citation.html" %} {% endblock sidebar %} {% block content %} diff --git a/templates/islandpick_select_genomes.html b/templates/islandpick_select_genomes.html index 0dd4819..7da3869 100644 --- a/templates/islandpick_select_genomes.html +++ b/templates/islandpick_select_genomes.html @@ -242,13 +242,13 @@ {% endblock %} {% block sidebar %} -

    Depending on the genomes selected for comparison, IslandPick will predict genomic islands of varying insertion ages.

    +

    Depending on the genomes selected for comparison, IslandPick will predict genomic islands of varying insertion ages.

    -

    If you don't see a genome, try changing the genome distance range.

    +

    If you don't see a genome, try changing the genome distance range.

    IslandPick Selection Parameters

    -

    Changing the IslandPick paremeters will change the genomes that are picked for comparison.

    +

    Changing the IslandPick paremeters will change the genomes that are picked for comparison.

    +

    Once you are satisfied with the genome selection please select your minimum island size and click "Run IslandPick".

    +

    Minimum Genomic Island Size

    - {% if nouploads %}

    We're sorry, custom analysis are currently disabled due to maintenance, please check back later.{% if message %}

    {{ message }}{% endif %}

    {% else %} + {% if nouploads %}

    We're sorry, custom analysis are currently disabled due to maintenance, please check back later.{% if message %}

    {{ message }}{% endif %}

    {% else %}

    {% endif %} diff --git a/templates/resources.html b/templates/resources.html index be9e68c..b673777 100644 --- a/templates/resources.html +++ b/templates/resources.html @@ -2,9 +2,9 @@ {% load static %} {% block sidebar %} -

    Please note that we have listed only those computational tools that refer to genomic island predictions as opposed to methods associated with horizontal gene transfer. In addition, we only list resources with websites or freely available software.

    +

    Please note that we have listed only those computational tools that refer to genomic island predictions as opposed to methods associated with horizontal gene transfer. In addition, we only list resources with websites or freely available software.

    -

    If you think a resource should be included in this list please contact us.

    +

    If you think a resource should be included in this list please contact us.

    {% endblock sidebar %} {% block content %} @@ -25,8 +25,8 @@

    Downloadable Software - tools that once installed locally, can be used to make predictions of genomic islands

    diff --git a/templates/results.html b/templates/results.html index 2a73787..beafd64 100644 --- a/templates/results.html +++ b/templates/results.html @@ -30,7 +30,7 @@ {% else %}  
    - + The analysis is not yet complete, please check back to this page in a while, or you will be notified by email when the analysis is complete if you elected to enter an email address.
    @@ -39,7 +39,7 @@  
     Legend:
    -  
    +  
         Pending
         Running
         Complete
    @@ -54,7 +54,7 @@ {% include "noanalysis.html" %} {% else %} {% if status == "Complete" %} - + @@ -65,21 +65,18 @@
    -
    -
    +
    +
    {{ genomename }}
    {% if ref_genome %}Aligned against reference genome {{ ref_genome }}
    {% endif %} -
     
    {% if default_analysis == False %}Note: This analysis was run using non-default parameters. See here for more details.
    {% endif %} @@ -93,14 +90,21 @@
    -
    - -
    -
    -
    - -
    -
    +
    +
    + +
    +
    + +
    + +
    + +
    + +
    +
    +
    diff --git a/templates/resultssidebar.html b/templates/resultssidebar.html index a37c2ce..fda2a48 100644 --- a/templates/resultssidebar.html +++ b/templates/resultssidebar.html @@ -1,5 +1,5 @@ {% load virulencefactors %} - +

    Predicted genomic islands and virulence/resistance gene annotations (when available) are coloured within the images based on the legend. Individual items for display can be selected below.

    {% if ref_genome %}Use caution when interpreting GI predictions for incomplete genomes. Gaps are indicated as grey bars in the circular plot, and any unaligned contigs are displayed at the end of the genome plot (indicated in grey on the circular alignment plot) and should be evaluated accordingly.{% endif %}
    @@ -29,7 +29,20 @@

     

    Toolbox -
    Visualize two genomes
    +
    +
    Search for gene:
    + +
    +
    +
    Visualize two genomes + +
    Show Islandpick Comparison Genomes
    Search Genes
    Download
    @@ -41,3 +54,7 @@
  • Artemis (with GenBank file) can be used to conduct further analysis of GIs. Artemis can be easily run using the web start version.
  • Mauve (using GenBank file) can be used to produce whole genome alignments and view conserved regions surronding GIs.
    • +

     

    + {% include "citation.html" %} + diff --git a/templates/selectgenome.html b/templates/selectgenome.html index 77e69de..91d36fd 100644 --- a/templates/selectgenome.html +++ b/templates/selectgenome.html @@ -1,45 +1,45 @@ {% extends "base.html" %} -{% load static %} +{% load static %} {% block headextras %} - - - - - + + + + + {% endblock %} {% block sidebar %} - -Please select a genome from the list. -Use the search box to bring matching genomes to the top of the list. - + {% include "citation.html" %} {% endblock %} {% block content %} -
    -IslandViewer
    - 
    -

    IslandViewer is a computational tool that integrates three different genomic island prediction methods: IslandPick, IslandPath-DIMOB, and SIGI-HMM. More Information. See our FAQs

    -
    - 
    -   Example, Example (incomplete genome) +
    + IslandViewer
    +  
    +

    IslandViewer is a computational tool that integrates three different genomic island prediction methods: IslandPick, IslandPath-DIMOB, and SIGI-HMM. More Information. See our FAQs

    +
    +  
    +    Example, Example (incomplete genome) +
     
     
    +News
     
    -

    News:

    +

    2016/01/21 - Small changes have been made to IslandViewer for improved clarity and better acknowledgement of past work. If you haven't already, check out the latest IslandViewer paper published last summer. Much more on improved visualization and genomic island predictions to come soon.

    +

    2015/12/08 - Service was disrupted to IslandViewer and the SFU emergency power supply on Tuesday, December 8 while planned repairs took place. We apologize for the inconvenience.

    2015/04/20 - Islandviewer 3 is now out of beta, however if you still need to access older analysis using IslandViewer 2 we will keep it available here for the next few months.

    -

    2015/03/03 - IslandViewer 3 has officially been released and is available here. IslandViewer 3 includes a new interactive genome visualization tool, IslandPlot, and expanded virulence factor, antimicrobial resistance gene, and pathogen-associated gene annotations, as well as homologs of these genes in closely related genomes. Notably, incomplete genomes are accepted as input in IslandViewer 3, though we strongly urge users to use complete genomes whenever possible. The old IslandViewer website will still be available for users to download results for any previously analyized custom genomes, but will eventually be replaced by IslandViewer 3. If you have any questions, comments, or issues with IslandViewer 3, please contact us.

    +

    2015/03/03 - IslandViewer 3 has officially been released and is available here. IslandViewer 3 includes a new interactive genome visualization tool, IslandPlot, and expanded virulence factor, antimicrobial resistance gene, and pathogen-associated gene annotations, as well as homologs of these genes in closely related genomes. Notably, incomplete genomes are accepted as input in IslandViewer 3, though we strongly urge users to use complete genomes whenever possible. The old IslandViewer website will still be available for users to download results for any previously analyized custom genomes, but will eventually be replaced by IslandViewer 3. If you have any questions, comments, or issues with IslandViewer 3, please contact us.

    2015/01/01 - Interactive IslandPlot visualizations are now available for circular and linear genomes views. In addition to this, more curated virulence and resistance gene annotations have been incorporated, as well as homologs of these genes as determined using the Resistance Gene Identifier (RGI) and a custom approach for virulence factors. An updated pathogen-associated genes analysis has also been complete for all available genomes.

    @@ -54,23 +54,23 @@  
     - -
    + +
    {% endblock content %} diff --git a/templates/upload.html b/templates/upload.html index 5313c57..9ab2ee2 100644 --- a/templates/upload.html +++ b/templates/upload.html @@ -331,7 +331,13 @@ document.getElementById('submitted').style.display = ''; } - + +

    Note for incomplete genomes

    +
    +

    Incomplete genomes are now accepted as input due to popular demand. However, whole genome analysis is still preferred to reduce false predictions and missing GIs. Please use at your own risk. We suggest to minimize the number of contigs before performing GI analysis and carefully evaluate all results from such custom jobs. Contigs will be ordered against a user-selected reference genome using the Mauve contig orderer (Rissman et al., 2009). Please note that annotation of the contigs is still required.

    +
    +  
    +

    Hints for a successful analysis

    Check and see if your genome file contains protein sequences for all CDSs AND the complete nucleotide sequence. A valid genome file should have full protein sequence data (under "\translation" tag within "CDS" primary tag) and nucleotide sequence data under ORIGIN or blank header in GENBANK or EMBL format, respectively. For example:

    @@ -367,6 +373,7 @@

    +

     

     

     

    diff --git a/templates/uploadsidebar.html b/templates/uploadsidebar.html index 670808a..0b453d1 100644 --- a/templates/uploadsidebar.html +++ b/templates/uploadsidebar.html @@ -1,6 +1,8 @@ - +

    We only accept user genomes that are formatted in EMBL or GENBANK format.

    -

    Note:Incomplete genomes are now accepted as input due to popular demand. However, whole genome analysis is still preferred to reduce false predictions and missing GIs. Please use at your own risk. We suggest to minimize the number of contigs before performing GI analysis and carefully evaluate all results from such custom jobs. Contigs will be ordered against a user-selected reference genome using the Mauve contig orderer (Rissman et al., 2009). Please note that annotation of the contigs is still required.

    For published genomes please see pre-computed results.

    Uploaded genomes and GI predictions will not be visible to other users of IslandViewer and will be available for at least 1 month.

    +
    +{% include "citation.html" %} + diff --git a/webui/models.py b/webui/models.py index 4db2192..22f014d 100644 --- a/webui/models.py +++ b/webui/models.py @@ -3,7 +3,7 @@ from django.db import models from django.conf import settings import pprint -from Bio.Phylo.TreeConstruction import _DistanceMatrix, DistanceTreeConstructor +#from Bio.Phylo.TreeConstruction import _DistanceMatrix, DistanceTreeConstructor from Bio import Phylo import StringIO import json diff --git a/webui/urls.py b/webui/urls.py index b9277da..0a6f96f 100644 --- a/webui/urls.py +++ b/webui/urls.py @@ -24,6 +24,7 @@ url(r'^resources/$', views.resources, name='resources'), url(r'^contactus/$', views.contactus, name='contactus'), url(r'^faq/$', views.faq, name='faq'), + url(r'^getMauve/$', views.getMauveFile,name='mauve'), url(r'^islandpick/$', views.islandpick, name='islandpick'), url(r'acknowledgements', views.acknowledgements, name='acknowledgements'), url(r'^plot/(?P\d+)/$', views.circularplotjs, name='circularplotjs'), diff --git a/webui/views.py b/webui/views.py index ff069cb..76c1b48 100644 --- a/webui/views.py +++ b/webui/views.py @@ -23,10 +23,11 @@ from collections import OrderedDict from webui.models import VIRULENCE_FACTORS, VIRULENCE_FACTOR_CATEGORIES from django.db import connection +from scripts import mauvewrap +import glob def index(request): return render(request, 'index.html') -# return HttpResponse("Hello, world. You're at the poll index.") def showgenomes(request): context = {} @@ -92,10 +93,10 @@ def results(request, aid): context['ref_genome'] = ref_genome.name elif(analysis.atype == Analysis.MICROBEDB): -# gpv_id = Replicon.objects.using('microbedb').filter(rep_accnum=analysis.ext_id)[0].gpv_id -# context['genomename'] = Genomeproject.objects.using('microbedb').get(pk=gpv_id).org_name +# gpv_id = Replicon.objects.using('microbedb').filter(rep_accnum=analysis.ext_id)[0].gpv_id +# context['genomename'] = Genomeproject.objects.using('microbedb').get(pk=gpv_id).org_name context['genomename'] = NameCache.objects.get(cid=analysis.ext_id).name -# context['genomename'] = 'Something from Microbedb' +# context['genomename'] = 'Something from Microbedb' # Fetch the virulence factors # island_genes = Genes.objects.filter(ext_id=analysis.ext_id).order_by('start').all() @@ -1241,7 +1242,30 @@ def fetchislandsfasta(request): response['Content-Disposition'] = "attachment; filename=\"gi_{0}.txt\"".format(filename) response.write(fasta) return response - + +def getMauveFile(request): + firstgenomeextid = request.GET.get('firstgenomeextid') + secondgenomeextid = request.GET.get('secondgenomeextid') + + firstgenomeextid = firstgenomeextid.split('.')[0] + secondgenomeextid = secondgenomeextid.split('.')[0] + + firstReplicon = Replicon.objects.using('microbedb').filter(rep_accnum__contains=firstgenomeextid)[0] + secondReplicon = Replicon.objects.using('microbedb').filter(rep_accnum__contains=secondgenomeextid)[0] + + firstGenomeProject = Genomeproject.objects.using('microbedb').get(gpv_id__exact=firstReplicon.gpv_id) + secondGenomeProject = Genomeproject.objects.using('microbedb').get(gpv_id__exact=secondReplicon.gpv_id) + + firstGbk = glob.glob(firstGenomeProject.gpv_directory+"/*"+".gbk")[0] + secondGbk = glob.glob(secondGenomeProject.gpv_directory+"/*"+".gbk")[0] + + mauveOutputPath = mauvewrap.getMauveResults(firstGbk,secondGbk) + + with open(mauveOutputPath,'r') as f: + data = f.read() + + return HttpResponse(data) + def about(request): return render(request, "about.html")