Add hide noise functionality

js/dgenies.js

 dgenies = {};
 dgenies.loading = "#loading";
+dgenies.noise = true;
 
 dgenies.notify = function (text, type="warning", delay=5000) {
     $.notify({

js/dgenies.result.controls.js

@@ -5,6 +5,7 @@ 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);
     $("form#select-zone input.submit").click(dgenies.result.controls.select_zone);
     $("form#export select").change(dgenies.result.export.export);
 };
@@ -33,6 +34,32 @@ dgenies.result.controls.launch_sort_contigs = function () {
     }, 0);
 };
 
+dgenies.result.controls.launch_hide_noise = function () {
+    d3.boxplot.zoom.reset_scale();
+    window.setTimeout(() => {
+        dgenies.show_loading("Building...");
+        window.setTimeout(() => {
+            dgenies.post(`/freenoise/${dgenies.result.id_res}`,
+                {noise: dgenies.noise ? 0 : 1},
+                function (data) {
+                    if (data["success"]) {
+                        dgenies.noise = !dgenies.noise;
+                        $("#hide-noise").val(dgenies.noise ? "Hide noise" : "Show noise");
+                        dgenies.reset_loading_message();
+                        window.setTimeout(() => {
+                            d3.boxplot.launch(data, true);
+                        }, 0);
+                    }
+                    else {
+                        dgenies.hide_loading();
+                        dgenies.notify(data["message"] || "An error occurred! Please contact us to report the bug", "danger");
+                    }
+                }
+            );
+        }, 0);
+    }, 0);
+};
+
 dgenies.result.controls.select_zone = function() {
     let contig_select = $("#select-contig").find(":selected");
     let target_select = $("#select-target").find(":selected");

lib/paf.py

@@ -5,6 +5,7 @@ import shutil
 from math import sqrt
 from numpy import mean
 from pathlib import Path
+from matplotlib import pyplot as plt
 
 
 class Paf:
@@ -76,7 +77,28 @@ class Paf:
         new_index_c, new_index_o = self.__flush_blocks(index_c, new_index_c, new_index_o, current_block)
         return new_index_c, new_index_o
 
-    def parse_paf(self, merge_index=True):
+    @staticmethod
+    def remove_noise(lines, noise_limit):
+        keep_lines = {
+            "0": [],
+            "1": [],
+            "2": [],
+            "3": []
+        }
+        for cls, c_lines in lines.items():
+            for line in c_lines:
+                print(line)
+                x1 = line[0]
+                x2 = line[1]
+                y1 = line[2]
+                y2 = line[3]
+                idy = line[4]
+                len_m = sqrt(pow(x2 - x1, 2) + pow(y2 - y1, 2))
+                if len_m >= noise_limit:
+                    keep_lines[cls].append(line)
+        return keep_lines
+
+    def parse_paf(self, merge_index=True, noise=True):
         min_idy = 10000000000
         max_idy = -10000000000
         lines = {
@@ -138,6 +160,7 @@ class Paf:
 
         len_q = q_abs_current_start
         len_t = t_abs_current_start
+        lines_lens = []
 
         try:
             with open(self.paf, "r") as paf_file:
@@ -159,6 +182,8 @@ class Paf:
                     y2 = int(parts[3]) + q_abs_start[v1]
                     x1 = int(parts[7 if strand == 1 else 8]) + t_abs_start[v6]
                     x2 = int(parts[8 if strand == 1 else 7]) + t_abs_start[v6]
+                    len_m = sqrt(pow(x2 - x1, 2) + pow(y2 - y1, 2))
+                    lines_lens.append(len_m)
                     if idy < self.limit_idy[0]:
                         class_idy = "0"
                     elif idy < self.limit_idy[1]:
@@ -172,6 +197,22 @@ class Paf:
             self.error = "PAF file does not exist!"
             return False
 
+        if not noise:
+            counts, bins, bars = plt.hist(lines_lens, bins=1000)
+            counts = list(counts)
+            max_value = max(counts)
+            max_index = counts.index(max_value)
+            limit_index = -1
+            print(max_value, max_index)
+            for i in range(max_index, len(counts)):
+                if counts[i] < max_value / 100:
+                    print("pass")
+                    limit_index = i
+                    break
+            print(limit_index)
+            if limit_index > -1:
+                lines = self.remove_noise(lines, bins[limit_index])
+
         self.parsed = True
         self.len_q = len_q
         self.len_t = len_t

requirements.txt

@@ -10,3 +10,4 @@ biopython==1.70
 python-crontab==2.2.*
 psutil==5.4.*
 tendo==0.2.*
+matplotlib==2.1.*

srv/main.py

@@ -209,6 +209,20 @@ def sort_graph(id_res):
     return jsonify({"success": False, "message": "Sort is not available for All-vs-All mode"})
 
 
+@app.route('/freenoise/<id_res>', methods=['POST'])
+def free_noise(id_res):
+    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")
+    paf = Paf(paf_file, idx1, idx2, False)
+    paf.parse_paf(noise=request.form["noise"] == "1")
+    if paf.parsed:
+        res = paf.get_d3js_data()
+        res["success"] = True
+        return jsonify(res)
+    return jsonify({"success": False, "message": paf.error})
+
+
 @app.route('/get-fasta-query/<id_res>', methods=['POST'])
 def build_fasta(id_res):
     res_dir = os.path.join(app_data, id_res)

srv/templates/results.html

@@ -64,6 +64,7 @@
                 <p><label>Regions delimiters:<br/>
                 <input type="range" min="0" max="5" value="2" step="1" id="chroms-limits"/></label></p>
                 <p><input type="button" id="sort-contigs" value="Sort contigs"/></p>
+                <p><input type="button" id="hide-noise" value="Hide noise"/></p>
             </form>
         </div>
     </div>