fix primer region bug

primerserver2/core/design_primer.py

@@ -38,6 +38,7 @@ def single(site):
                 'SEQUENCE_TEMPLATE': template,
                 type: [pos,length]
             })
+        p3['SEQUENCE_RELATIVE_TARGET_START'] = pos
         return([{'id': id, 'primers': p3}])
     if type=='FORCE_END':
         p3_settings['PRIMER_MIN_LEFT_THREE_PRIME_DISTANCE'] = -1
@@ -49,6 +50,7 @@ def single(site):
                 'SEQUENCE_TEMPLATE': template,
                 'SEQUENCE_FORCE_LEFT_END': pos
             })
+        p3_L['SEQUENCE_RELATIVE_TARGET_START'] = pos
 
         p3_settings['PRIMER_MIN_LEFT_THREE_PRIME_DISTANCE'] = 3
         p3_settings['PRIMER_MIN_RIGHT_THREE_PRIME_DISTANCE'] = -1
@@ -59,6 +61,7 @@ def single(site):
                 'SEQUENCE_TEMPLATE': template,
                 'SEQUENCE_FORCE_RIGHT_END': pos
             })
+        p3_R['SEQUENCE_RELATIVE_TARGET_START'] = pos
 
         return([{'id': id+'-LEFT', 'primers': p3_L},
                 {'id': id+'-RIGHT', 'primers': p3_R}

primerserver2/core/make_primers.py

@@ -52,6 +52,7 @@ def make_primers(query):
         primers[id][f'PRIMER_LEFT_{rank}_GC_PERCENT'] = calculate_GC(seq_F)
         primers[id][f'PRIMER_RIGHT_{rank}_GC_PERCENT'] = calculate_GC(seq_R)
         primers[id][f'PRIMER_PAIR_{rank}_PRODUCT_SIZE'] = -1
+        primers[id]['SEQUENCE_RELATIVE_TARGET_START'] = 0
 
     return primers
 

primerserver2/data/p3_settings.json

@@ -1,16 +1,16 @@
 {
     "PRIMER_EXPLAIN_FLAG": 1,
     "PRIMER_NUM_RETURN": 30,
-    "PRIMER_MIN_SIZE": 18,
+    "PRIMER_MIN_SIZE": 14,
     "PRIMER_OPT_SIZE": 20,
-    "PRIMER_MAX_SIZE": 23,
+    "PRIMER_MAX_SIZE": 28,
     "PRIMER_MIN_TM": 57.0,
     "PRIMER_OPT_TM": 60.0,
     "PRIMER_MAX_TM": 63.0,
     "PRIMER_PAIR_MAX_DIFF_TM": 3.0,
-    "PRIMER_MIN_GC": 35.0,
+    "PRIMER_MIN_GC": 20.0,
     "PRIMER_OPT_GC_PERCENT": 50.0,
-    "PRIMER_MAX_GC": 65.0,
+    "PRIMER_MAX_GC": 80.0,
     "PRIMER_MAX_END_STABILITY": 9.0,
     "PRIMER_MIN_LEFT_THREE_PRIME_DISTANCE": 3,
     "PRIMER_MIN_RIGHT_THREE_PRIME_DISTANCE": 3,

primerserver2/web/run.py

@@ -23,6 +23,9 @@ def progress():
 bp = Blueprint('run', __name__)
 @bp.route('/run', methods=['POST'])
 def run():
+    ###################  init #############################
+    global_var.init()
+
     ###################  Design primers ###################
     query_string = request.form['query']
     dbs = [db_dir+'/'+x for x in request.form['selected_dbs'].split(',')]
@@ -49,7 +52,6 @@ def run():
 
     ###################  Checking specificity  #############
     if request.form['app-type']!='design':
-        global_var.init()
         primers = run_blast.run_blast_parallel(primers=primers, dbs=dbs, cpu=web_config['cpu'],\
             checking_size_max=int(request.form['checking_size_max']), checking_size_min=int(request.form['checking_size_min']), \
                 report_amplicon_seq=bool(int(request.form['report_amplicon_seqs'])), Tm_diff=int(request.form['Tm_diff']), \
@@ -60,4 +62,5 @@ def run():
 
 @bp.route('/monitor')
 def monitor():
+    time.sleep(1)
     return Response(progress(), mimetype= 'text/event-stream')

primerserver2/web/static/js/generate_html_result.js

@@ -42,6 +42,8 @@ function generate_html_result(selected_dbs, db_name_change, data){
         $('#primers-result').append($('#primers-result-template-site').html());
         $('#primers-result-template-site').html(raw_html_site);
 
+        var retrieve_start = site_pos - result_data[site_id]['SEQUENCE_RELATIVE_TARGET_START']
+
         // primer
         for (var i=0; i<primer_num; i++) {
             var raw_html_primer = $('#primers-result-template-primer').html();
@@ -65,7 +67,7 @@ function generate_html_result(selected_dbs, db_name_change, data){
                 .html('Primer '+primer_rank);
 
             var p_start = result_data[site_id]['PRIMER_LEFT_'+raw_rank][0]+1;
-            p_start = p_start==0 ? '' : p_start;
+            p_start = p_start==0 ? '' : p_start+retrieve_start;
             var p_len = result_data[site_id]['PRIMER_LEFT_'+raw_rank][1];
             var p_end = p_start=='' ? '' : p_start+p_len-1;
             $('#primers-result-template-primer .primer-seq-detail')
@@ -78,7 +80,7 @@ function generate_html_result(selected_dbs, db_name_change, data){
                     +'</tr>')
 
             p_start = result_data[site_id]['PRIMER_RIGHT_'+raw_rank][0]+1;
-            p_start = p_start==0 ? '' : p_start;
+            p_start = p_start==0 ? '' : p_start+retrieve_start;
             p_len = result_data[site_id]['PRIMER_RIGHT_'+raw_rank][1];
             p_end = p_start=='' ? '' : p_start+p_len-1;
             $('#primers-result-template-primer .primer-seq-detail')