sample_set.py stats_decorator.py add loci list

See #3456

server/web2py/applications/vidjil/controllers/sample_set.py

@@ -659,6 +659,7 @@ def getStatHeaders():
     b = BooleanDecorator()
     p = BarDecorator()
     bc = BarChartDecorator()
+    l = LociListDecorator()
     return [('sample_sets', 'db', s),
             ('main_clone', 'parser', m),
             ('reads', 'parser', m),
@@ -666,6 +667,7 @@ def getStatHeaders():
             ('mapped_percent', 'parser', p),
             ('bool', 'parser', b),
             ('bool_true', 'parser', b),
+            ('loci', 'parser', l),
             ('genescan', 'parser', bc)
         ]
 
@@ -698,6 +700,7 @@ def getFusedStats(file_name, res, dest):
     dest['mapped_percent'] = 100.0 * (float(data['reads']['segmented'][result_index])/float(reads))
     dest['bool'] = False
     dest['bool_true'] = True
+    dest['loci'] = [x for x in data['reads']['germline'] if data['reads']['germline'][x][result_index] >= 0]
     dest['genescan'] = [68, 27, 18, 45, 89, 63, 53, 64, 93, 21, 47,  5, 64, 68, 46, 68, 18,
         72, 36, 70, 39, 21, 84, 32, 29,  4, 76, 51, 33, 67, 14, 57, 75, 61,
         29, 11, 81, 71, 91, 32, 40, 71, 87, 54, 50, 88, 72, 59, 29, 80, 48,

server/web2py/applications/vidjil/models/stats_decorator.py

@@ -51,3 +51,15 @@ class SetsDecorator(StatDecorator):
             d = DIV("(%d) %s" % (sample_set['id'], sample_set['name']))
             ssets.append(d)
         return DIV(*ssets)
+
+class LociListDecorator(StatDecorator):
+
+    def __init__(self):
+        super(LociListDecorator, self).__init__()
+
+    def decorate(self, data):
+        loci = []
+        for locus in data:
+            span = SPAN(locus)
+            loci.append(span)
+        return DIV(*loci)