Add sort functionnality

js/d3.boxplot.controls.js

@@ -8,11 +8,24 @@ d3.boxplot.controls.init = function () {
 };
 
 d3.boxplot.controls.launch_sort_contigs = function () {
-    alert("Not supported yet!");
-    $.post(`/sort/${d3.boxplot.id_res}`,
-        {},
-        function (data) {
-            console.log(data);
-        }
-    );
+    $("#loading").find(".mylabel").html("Building...");
+    $("#loading").show();
+    window.setTimeout(() => {
+            $.post(`/sort/${d3.boxplot.id_res}`,
+                {},
+                function (data) {
+                    if (data["success"]) {
+                        $("#loading").find(".mylabel").html("Loading...");
+                        window.setTimeout(() => {
+                            d3.boxplot.launch(data, true);
+                        }, 0);
+                    }
+                    else {
+                        $("#loading").find(".mylabel").html("Loading...");
+                        $("#loading").hide();
+                        alert("An error occurred!");
+                    }
+                }
+            );
+        }, 0);
 };
\ No newline at end of file

js/d3.boxplot.js

@@ -73,7 +73,7 @@ d3.boxplot.init = function (id, from_file=false) {
     }
 };
 
-d3.boxplot.launch = function(res) {
+d3.boxplot.launch = function(res, update=false) {
     d3.boxplot.name_x = res["name_x"];
     d3.boxplot.name_y = res["name_y"];
     d3.boxplot.lines = res["lines"];
@@ -83,11 +83,13 @@ d3.boxplot.launch = function(res) {
     d3.boxplot.max_idy = res["max_idy"];
     d3.boxplot.limit_idy = res["limit_idy"];
     d3.boxplot.draw(res["x_contigs"], res["x_order"], res["y_contigs"], res["y_order"]);
-    $("div#draw").resizable({
-        aspectRatio: true
-    });
-    d3.boxplot.events.init();
-    d3.boxplot.controls.init();
+    if (!update) {
+        $("div#draw").resizable({
+            aspectRatio: true
+        });
+        d3.boxplot.events.init();
+        d3.boxplot.controls.init();
+    }
 };
 
 d3.boxplot.select_zone = function (x, y) {
@@ -537,6 +539,7 @@ d3.boxplot._sort_color_idy = function(a, b) {
 };
 
 d3.boxplot.draw_legend = function () {
+    d3.select("#legend .draw").html(""); //Empty legend
     let color_idy = d3.boxplot.color_idy;
     let color_idy_len = Object.keys(color_idy).length;
     let color_idy_order = ["pos+", "pos-", "neg+", "neg-"];

lib/paf.py

 #!/usr/bin/env python3
 
+from math import sqrt
+
 
 class Paf:
     limit_idy = 0.5
@@ -13,11 +15,11 @@ class Paf:
         self.len_t = None
         self.min_idy = None
         self.max_idy = None
-        self.lines = None
-        self.q_contigs = None
-        self.q_order = None
-        self.t_contigs = None
-        self.t_order = None
+        self.lines = {}
+        self.q_contigs = {}
+        self.q_order = []
+        self.t_contigs = {}
+        self.t_order = []
         self.name_q = None
         self.name_t = None
         self.parsed = False
@@ -102,7 +104,7 @@ class Paf:
                         class_idy = "pos-"
                     else:
                         class_idy = "pos+"
-                    lines[class_idy].append([x1, x2, y1, y2, idy])
+                    lines[class_idy].append([x1, x2, y1, y2, idy, v1, v6])
         except IOError:
             self.error = "PAF file does not exist!"
             return False
@@ -144,3 +146,60 @@ class Paf:
                 out_f.write(json.dumps(data))
         else:
             raise Exception(data)
+
+    def sort(self):
+        gravity_contig = {}
+        lines_on_block = {}
+        # Compute size of blocks (in term of how many big match they have), and save median of each match on each one
+        # (for next step)
+        for line in [j for i in list(self.lines.values()) for j in i]:
+            x1 = int(line[0])
+            x2 = int(line[1])
+            y1 = int(line[2])
+            y2 = int(line[3])
+            idy = int(line[4])
+            contig = line[5]
+            chrm = line[6]
+            block = (contig, chrm)
+            med_q = x1 + (abs(x2 - x1) / 2)
+            len_m = sqrt(pow(x2 - x1, 2) + pow(y2 - y1, 2))  # Pow of len
+            len_m_2 = pow(1 + len_m, 2)
+            if block not in lines_on_block:
+                lines_on_block[block] = []
+            lines_on_block[block].append((med_q, len_m_2))
+
+            if contig not in gravity_contig:
+                gravity_contig[contig] = {}
+            if chrm not in gravity_contig[contig]:
+                gravity_contig[contig][chrm] = 0
+            gravity_contig[contig][chrm] += len_m_2
+
+        # For each contig, find best block, and deduce gravity of contig:
+        gravity_on_contig = {}
+        for contig, chr_blocks in gravity_contig.items():
+            # Find best block:
+            max_number = 0
+            max_chr = None
+            for chrm, size in chr_blocks.items():
+                if size > max_number:
+                    max_number = size
+                    max_chr = chrm
+
+            # Compute gravity of contig:
+            nb_items = 0
+            sum_items = 0
+            for med in lines_on_block[(contig, max_chr)]:
+                sum_items += med[0] * med[1]
+                nb_items += med[1]
+            gravity_on_contig[contig] = sum_items / nb_items
+
+        # Sort contigs:
+        self.q_order.sort(key=lambda x: gravity_on_contig[x] if x in gravity_on_contig else self.len_q + 1000)
+
+        with open(self.idx_q, "w") as idx_q_f:
+            idx_q_f.write(self.name_q + "\n")
+            for contig in self.q_order:
+                print(contig)
+                idx_q_f.write("\t".join([contig, str(self.q_contigs[contig])]) + "\n")
+        self.parsed = False
+        self.parse_paf()

srv/main.py

@@ -156,7 +156,17 @@ def get_graph():
 
 @app.route('/sort/<id_res>', methods=['POST'])
 def sort_graph(id_res):
-    pass
+    paf = 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")
+    paf = Paf(paf, idx1, idx2)
+    paf.sort()
+    if paf.parsed:
+        res = paf.get_d3js_data()
+        res["success"] = True
+        return jsonify(res)
+    return jsonify({"success": False, "message": paf.error})
+
 
 if __name__ == '__main__':
     app.run()