Add summary stats, Implements #18

src/dgenies/lib/paf.py

@@ -8,6 +8,7 @@ from pathlib import Path
 import matplotlib as mpl
 mpl.use('Agg')
 from matplotlib import pyplot as plt
+import json
 
 
 class Paf:
@@ -128,10 +129,10 @@ class Paf:
         min_idy = 10000000000
         max_idy = -10000000000
         lines = {
-            "0": [],
-            "1": [],
-            "2": [],
-            "3": []
+            "0": [],  # idy < 0.25
+            "1": [],  # idy < 0.5
+            "2": [],  # idy < 0.75
+            "3": []  # idy > 0.75
         }
         try:
             name_q, q_order, q_contigs, q_reversed, q_abs_start, q_abs_current_start, q_len = self.load_index(
@@ -508,12 +509,35 @@ class Paf:
         Get summary of identity
         :return: table with percents by category
         """
+        summary_file = self.paf + ".summary"
+        if os.path.exists(summary_file):
+            with open(summary_file, "r") as summary_file:
+                txt = summary_file.read()
+                return json.loads(txt)
         self.parse_paf(False, False)
+        if self.parsed:
             percents = {}
-        total = 0
-        for cat in self.lines:
-            nb_lines = len(self.lines[cat])
-            percents[cat] = nb_lines
-            total += nb_lines
-        for cat in self.lines:
-            percents[cat] /= total
+            position_idy = {}
+
+            cats = sorted(self.lines.keys())
+
+            for cat in cats:
+                for line in self.lines[cat]:
+                    position_idy.update(position_idy.fromkeys(range(line[0], line[1]+1), cat))
+                percents[cat] = 0
+
+            import time
+            start = time.time()
+
+            total = self.len_t
+            percents["-1"] = (total - len(position_idy)) / total * 100
+
+            position_idy_values = list(position_idy.values())
+            for cat in cats:
+                percents[cat] = position_idy_values.count(cat) / total * 100
+
+            with open(summary_file, "w") as summary_file:
+                summary_file.write(json.dumps(percents))
+
+            return percents
+        return None

src/dgenies/static/js/d3.boxplot.js

@@ -34,7 +34,8 @@ d3.boxplot.color_idy = {
     "3": "#094b09",
     "2": "#2ebd40",
     "1": "#d5670b",
-    "0": "#ffd84b"
+    "0": "#ffd84b",
+    "-1": "#fff"
 };
 d3.boxplot.limit_idy = null;
 d3.boxplot.min_idy_draw = 0;

src/dgenies/static/js/dgenies.result.controls.js

@@ -6,10 +6,28 @@ dgenies.result.controls = {};
 dgenies.result.controls.init = function () {
     $("#sort-contigs").click(dgenies.result.controls.launch_sort_contigs);
     $("#hide-noise").click(dgenies.result.controls.launch_hide_noise);
+    $("#summary").click(dgenies.result.controls.summary);
     $("form#select-zone input.submit").click(dgenies.result.controls.select_zone);
     $("form#export select").change(dgenies.result.export.export);
 };
 
+dgenies.result.controls.summary = function () {
+    dgenies.show_loading("Building...");
+    window.setTimeout(() => {
+        dgenies.post(`/summary/${dgenies.result.id_res}`,
+            {},
+            function (data) {
+                dgenies.hide_loading();
+                if (data["success"]) {
+                    dgenies.result.summary.show(data["percents"]);
+                }
+                else {
+                    dgenies.notify(data["message"] || "An error occurred! Please contact us to report the bug", "danger");
+                }
+            })
+    }, 0);
+};
+
 dgenies.result.controls.launch_sort_contigs = function () {
     d3.boxplot.zoom.reset_scale();
     window.setTimeout(() => {

src/dgenies/static/js/dgenies.result.summary.js

+if (!dgenies || !dgenies.result) {
+    throw "dgenies.result wasn't included!"
+}
+dgenies.result.summary = {};
+
+dgenies.result.summary.show = function(percents) {
+    console.log(percents);
+    let svgcontainer = d3.select("#draw-stats").html("").append("svg:svg")
+        .attr("width", "500px")
+        .attr("height", "220px");
+    let container = svgcontainer.append("svg:g");
+    let percents_order = ["-1", "0", "1", "2", "3"];
+    let x = 0;
+    let percent_value = 0;
+    for (let i in percents_order) {
+        let percent = percents_order[i];
+        let label="";
+        switch (percent) {
+            case "-1":
+                label = "No match";
+                break;
+            case "0":
+                label = "< 25 %";
+                break;
+            case "1":
+                label = "< 50 %";
+                break;
+            case "2":
+                label = "< 75 %";
+                break;
+            case "3":
+                label = "> 75 %";
+                break;
+        }
+        console.log(percent);
+        x += percent_value;
+        percent_value = percents[percent];
+        container.append("rect")
+            .attr("x", x + "%")
+            .attr("y", 0)
+            .attr("width", percent_value + "%")
+            .attr("height", "50px")
+            .attr("stroke", "none")
+            .attr("fill", d3.boxplot.color_idy[percent]);
+        container.append("rect")
+            .attr("x", 5)
+            .attr("y", 70 + (i * 30))
+            .attr("width", "10px")
+            .attr("height", "10px")
+            .attr("fill", d3.boxplot.color_idy[percent])
+            .style("stroke", "#000")
+            .style("stroke-width", "1px");
+        container.append("text")
+            .attr("x", 30)
+            .attr("y", 82 + (i * 30))
+            .attr("font-family", "sans-serif")
+            .attr("font-size", "12pt")
+            .text(label + ":");
+        container.append("text")
+            .attr("x", 110)
+            .attr("y", 82 + (i * 30))
+            .attr("font-family", "sans-serif")
+            .attr("font-size", "12pt")
+            .text(percent_value.toFixed(2) + " %");
+    }
+
+    container.append("rect")
+        .attr("x", 0)
+        .attr("y", 0)
+        .attr("width", "100%")
+        .attr("height", "50px")
+        .style("stroke", "#000")
+        .style("fill", "none")
+        .style("stroke-width", "1px");
+
+    $("#modal-stats").dialog({
+        title: "Summary of identity",
+        width: "550px",
+        buttons: [{
+            text: "Export PNG",
+            click: dgenies.result.summary.export_png
+        },{
+            text: "Export SVG",
+            click: dgenies.result.summary.export_svg
+        },{
+            text: "Close",
+            click: function() {
+                $(this).dialog("close");
+            }
+        }]
+    })
+};
+
+dgenies.result.summary.get_svg = function () {
+    return $("#draw-stats").html();
+};
+
+dgenies.result.summary.save_file = function (blob, format) {
+    saveAs(blob, `summary_${d3.boxplot.name_y}_to_${d3.boxplot.name_x}.${format}`);
+};
+
+dgenies.result.summary.export_svg = function () {
+    let blob = new Blob([dgenies.result.summary.get_svg()], {type: "image/svg+xml"});
+    dgenies.result.summary.save_file(blob, "svg");
+};
+
+dgenies.result.summary.export_png = function () {
+    let export_div = $("div#export-pict");
+    export_div.html("").append($("<canvas>"));
+    canvg(export_div.find("canvas")[0], dgenies.result.summary.get_svg());
+    let canvas = export_div.find("canvas")[0];
+    canvas.toBlob(function(blob) {
+        dgenies.result.summary.save_file(blob, "png");
+        export_div.html("");
+    }, "image/png");
+};
\ No newline at end of file

src/dgenies/templates/base.html

@@ -5,10 +5,10 @@
     <title>{{ title }}</title>
     {% block scripts %}
         <script src="{{ url_for('static', filename='js/jquery-3.2.1.min.js') }}" type="text/JavaScript"></script>
-        <script src="{{ url_for('static', filename='js/jquery-ui.min.js') }}" type="text/JavaScript"></script>
         <script src="{{ url_for('static', filename='js/popper.min.js') }}" type="text/JavaScript"></script>
         <script src="{{ url_for('static', filename='js/bootstrap.min.js') }}" type="text/JavaScript"></script>
         <script src="{{ url_for('static', filename='js/bootstrap-notify.min.js') }}" type="text/JavaScript"></script>
+        <script src="{{ url_for('static', filename='js/jquery-ui.min.js') }}" type="text/JavaScript"></script>
         <script src="{{ url_for('static', filename='js/dgenies.js') }}" type="text/JavaScript"></script>
         <script src="{{ url_for('static', filename='js/dgenies.prototypes.js') }}" type="text/JavaScript"></script>
     {% endblock %}

src/dgenies/templates/result.html

@@ -7,6 +7,7 @@
     <script src="{{ url_for('static', filename='js/dgenies.result.js') }}" type="text/JavaScript"></script>
     <script src="{{ url_for('static', filename='js/dgenies.result.controls.js') }}" type="text/JavaScript"></script>
     <script src="{{ url_for('static', filename='js/dgenies.result.export.js') }}" type="text/JavaScript"></script>
+    <script src="{{ url_for('static', filename='js/dgenies.result.summary.js') }}" type="text/JavaScript"></script>
     <script src="{{ url_for('static', filename='js/d3.min.js') }}" type="text/JavaScript"></script>
     <script src="{{ url_for('static', filename='js/d3.boxplot.js') }}" type="text/JavaScript"></script>
     <script src="{{ url_for('static', filename='js/d3.boxplot.zoom.js') }}" type="text/JavaScript"></script>
@@ -83,5 +84,8 @@
         </div>
     </div>
     <div id="export-pict" style="display: none;"></div>
+    <div id="modal-stats" style="display: none;">
+        <div id="draw-stats" style="margin-top: 15px"></div>
+    </div>
 </div>
 {% endblock %}
\ No newline at end of file

src/dgenies/views.py

@@ -375,7 +375,26 @@ def no_assoc(id_res):
 
 @app.route('/summary/<id_res>', methods=['POST'])
 def summary(id_res):
-    pass
+    paf_file = os.path.join(APP_DATA, id_res, "map.paf")
+    idx1 = os.path.join(APP_DATA, id_res, "query.idx")
+    idx2 = os.path.join(APP_DATA, id_res, "target.idx")
+    try:
+        paf = Paf(paf_file, idx1, idx2, False)
+    except FileNotFoundError:
+        return jsonify({
+            "success": False,
+            "message": "Unable to load data!"
+        })
+    percents = paf.get_summary_stats()
+    if percents is None:
+        return jsonify({
+            "success": False,
+            "message": "Build of summary failed. Please contact us to report the bug"
+        })
+    return jsonify({
+        "success": True,
+        "percents": percents
+    })
 
 
 @app.route("/ask-upload", methods=['POST'])