clone; add a new axis segment ratio and his method inside clone.js

Return the percentage value of germline sequence covered by clonotype sequence
Exclusion of CDR3 junction deletion

browser/js/axis_conf.js

@@ -78,6 +78,9 @@ AXIS_SCATTERPLOT = ["V/5' gene",
                     "J/3' del'",
                     "V/5' length",
                     "J/3' length",
+                    "V/5' ratio",
+                    "D/4' ratio",
+                    "J/3' ratio",
                     "[cloneDB] Hits (sample)",
                     "[cloneDB] Hits (set)",
                     "Main sample"
@@ -196,6 +199,28 @@ AXIS_DEFAULT = {
         sort :      "alphanumerical",
         autofill:   false
     },
+    "V/5' ratio": {
+        doc:        "Proportion of V/5' germline sequence covered by clonotype sequencing (exclude CDR3 deletion)",
+        fct:        function(clone) {
+                        return clone.getGermlineRatio('5')
+                        // var feature = clone.getSegFeature('5')
+                    },
+        autofill:   true
+    },
+    "D/4' ratio": {
+        doc:        "Proportion of D/4' germline sequence covered by clonotype sequencing (exclude CDR3 deletion)",
+        fct:        function(clone) {
+                        return clone.getGermlineRatio('4')
+                    },
+        autofill:   true
+    },
+    "J/3' ratio": {
+        doc:        "Proportion of J/3' germline sequence covered by clonotype sequencing (exclude CDR3 deletion)",
+        fct:        function(clone) {
+                        return clone.getGermlineRatio('3')
+                    },
+        autofill:   true
+    },
     "Sequence length" : {
         doc:        "length of the consensus sequence of the clonotype",
         fct:        function(clone) {return clone.getSequenceLength()},

browser/js/clone.js

@@ -1000,6 +1000,39 @@ Clone.prototype = {
         return fasta
     },
 
+    /**
+     * Return the percentage of germline gene covered by the segment
+     * TODO: See if we should take into account deletion and how. (my recommandation is to don't include deletion in value)
+     * TODO: controle case with up/down sequence ?
+     * @param {string} gene_way 
+     * @returns undefined if not segment, percentage of covered sequence 
+     */
+    getGermlineRatio: function(gene_way) {
+
+        var gene     = this.getGene(gene_way);
+        var germName = this.germline.substring(0, 3);
+        if (this.germline != undefined) {
+            seq_germ = this.m.findGermlineFromGene(gene)
+            seq_germ = (seq_germ != undefined) ? seq_germ.replaceAll(".","") : undefined
+        }
+
+        if (!this.hasSeg('3', '5')) {
+            return undefined
+        }
+        if (gene_way == "5") {
+            seq_clone = this.sequence.substring(this.seg['5'].start != undefined ? this.seg['5'].start : 0,  this.seg['5'].stop+1)
+            seq_germ_length = seq_germ.length - this.seg['5'].delRight
+        } else if (gene_way == '4' && this.seg['4']){
+            seq_clone = this.sequence.substring(this.seg['4'].start,  this.seg['4'].stop)
+            seq_germ_length = seq_germ.length - this.seg['4'].delLeft - this.seg['4'].delRight
+        } else if (gene_way == '3'){
+            seq_clone = this.sequence.substring(this.seg['3'].start, this.seg['3'].stop? this.seg['3'].stop+1 : this.sequence.length)
+            seq_germ_length = seq_germ.length - this.seg['3'].delLeft
+        }
+
+        return (seq_clone.length / seq_germ_length)*100
+    },
+
     /**
      * compute the clone size (**only the main sequence, without merging**) at a given time
      * @param {integer} time - tracking point (default value : current tracking point)