add data from circ2disease, connect circRNA with disease

cirDraw/restart_uwsgi.sh

@@ -6,4 +6,4 @@ sudo uwsgi --ini /home/circ/circDraw/cirDraw/uwsgi.ini --uid circ --enable-threa
 cd /home/circ/circDraw/process_watchdog/
 python3 resetdb.py admin_login.json clean
 
-#> /var/log/uwsgi/circDraw.log
+> /var/log/uwsgi/circDraw.log

cirDraw/static/tools/js/drawCirc.js

@@ -507,6 +507,7 @@ function drawCircRNA(exonComponents, circStart, circEnd) {
     for (i = 0, up = exons.length; i < up; i++) {
         var start = exons[i].start,
             end = exons[i].end,
+            disease = exons[i].disease,
             exStartAngle = startAngle,
             exEndAngle = startAngle + ((end - start) / len) * 360,
             type = exons[i].type,
@@ -831,7 +832,8 @@ function drawArc(data) {
         infobox = infoBox(x, y, {
             name: $chr.text() + ' : ' + data.start + ' - ' + data.end,
             position: data.start + "-" + data.end,
-            source: data.source
+            source: data.source,
+            disease: data.disease,
         });
     }).mouseout(function () {
         Snap.animate(5, 1, function (val) {

cirDraw/static/tools/js/upload.js

@@ -187,6 +187,8 @@ $(document).ready(function () {
                             status = reportID[0].save_status;
                         //console.log(reportID, status);
                         if (status === false) {
+                            $('.lds-roller').remove();
+                            $('#upload-text').remove();
                             $('#processtip').html('<p>Processing Failed! Wrong file type or server failed. Please <a id="refresher" onclick="location.reload()"><i>refresh</i><i class="fas fa-redo-alt ml-1"></i></a></p>');
                             $('#refresher').hover(function(){
                                 $('#refresher').css({'cursor':'pointer', 'color': '#fed136'});

cirDraw/tools/handle_file.py

@@ -216,11 +216,20 @@ def process_file(file, assembly: str, file_type, task_id, bias=2):
                             print('demjson decode ERROR:', e)
                         for i in components:
                             i['mods'] = ujson.loads(i['mods'])
+                        with connection.cursor() as cur:
+                            cur.execute(f'select disease from circ_disease where assembly="{assembly}" and chr_num="{chr_num}" and start>={start-bias} and start<={start+bias} and end<={end+bias} and end>={end-bias};')
+                            disease = cur.fetchall()
+                        print(disease)
+                        if len(disease) == 0:
+                            disease = 'Unknown'
+                        else:
+                            disease = disease[0]
                         circ_json = {"start": int(circ[3]),
                                 "end": int(circ[4]),
                                 "source": "CIRCpedia V2",
                                 "gene": circ[0],
                                 "transcript": circ[1],
+                                "disease": disease,
                                 "components": components}
                         #print('This is gene of circ', circ[0])
 
@@ -268,12 +277,21 @@ def process_file(file, assembly: str, file_type, task_id, bias=2):
                 for i in components:
                     i['mods'] = ujson.loads(i['mods'])
                 #print('alter components')
+                with connection.cursor() as cur:
+                    cur.execute(f'select disease from circ_disease where assembly="{assembly}" and chr_num="{chr_num}" and start>={start-bias} and start<={start+bias} and end<={end+bias} and end>={end-bias};')
+                    disease = cur.fetchall()
+                if len(disease) == 0:
+                    disease = 'Unknown'
+                else:
+                    disease = disease[0]
+
                 try:
                     circ_on_gene[gene][1].append({"start": int(circ[1]),
                                                         "end": int(circ[2]),
                                                         "source": "circDraw_annotated",
                                                         "gene": gene,
                                                         "transcript": transcript,
+                                                        "disease": disease,
                                                         "components": components})
                 except:
                         # get gene info
@@ -288,6 +306,7 @@ def process_file(file, assembly: str, file_type, task_id, bias=2):
                                                             "source": "circDraw_annotated",
                                                             "gene": gene,
                                                             "transcript": transcript,
+                                                            "disease": disease,
                                                             "components": components}]]
                     except Exception as e:
                         print("Add circ error:", e)

cirDraw/tools/models.py

@@ -20,6 +20,20 @@ class Meta:
         db_table = 'chromosome_length'
         managed = False
 
+class circ_disease(models.Model):
+    """Store known chromosome length, fixed by existed knowledge."""
+    id = models.AutoField(primary_key=True)
+    assembly = models.CharField(max_length=100)
+    chr_num = models.CharField(max_length=50)
+    start = models.IntegerField()
+    end = models.IntegerField()
+    name = models.CharField(max_length=255)
+    disease = models.CharField(max_length=255)
+
+    class Meta:
+        db_table = 'circ_disease'
+        managed = False
+
 # Species genome
 _assembly = ['hg19', 'hg38', 'rn6', 'danRer11', 'sacCer3', 'mm10']
 

process_watchdog/resetdb.py

@@ -91,7 +91,10 @@ def cleandb_except(connector, exception_box, exceptions):
     # delete from table where exceptions won't be deleted.
     operator = mc.Operator(connector)
     for t in exception_box:
-        operator.clean_table(t, {'md5': ['!=', exceptions]})
+        if exceptions != '':
+            operator.clean_table(t, {'md5': ['!=', exceptions]})
+        else:
+            operator.clean_table(t)
         print('Exception drop Success in ', t)
     operator.terminate()
 
@@ -142,7 +145,7 @@ def main(login_file_name, inp):
 
     elif inp == "clean":
         clean_box = ['tools_species_circrnas', 'tools_species_genome_exons_introns', 'tools_species_genome_genes', 'tools_species_genome_transcripts']
-        example_md5 = '8bd10a77cbda74ed2513d2643a39b0bb'
+        example_md5 = ''#'8bd10a77cbda74ed2513d2643a39b0bb'
         path_box = ["../cirDraw/media/md5_data/"]
         empty_db(connector, clean_box)
         empty_dir(path_box)

related_genome_info/process_pkg/mysqlconnect.py

@@ -211,7 +211,7 @@ def create_table_core(self, table_name, table_columns):
 
 
     # auto-clean
-    def autoclean(self, timenow):
+    #def autoclean(self, timenow):