Merge branch 'feature-tc/3943-implement-null-for-normalized_reads' into 'dev'

Resolve "Implement null for normalized_reads"

Closes #3943

See merge request !485

algo/tests/data/results-two-clones-1-3.vidjil

@@ -27,6 +27,7 @@
 	    "sequence" : "seq-1",
 
 	    "reads" :  [ 300 ] ,
+        "normalized_reads" :  [ 500 ] ,
 	    "top" : 1,
 	    "germline" : "IGH"
 	},

browser/js/model.js

@@ -699,8 +699,11 @@ changeAlleleNotation: function(alleleNotation) {
      * if raw is defined, do not normalize
      */
     normalize_reads: function(clone, time, raw) {
-      if (this.normalization_mode == this.NORM_EXTERNAL && clone.normalized_reads != undefined && raw == undefined) {
-        return clone.normalized_reads[time] ;
+      if (this.normalization_mode == this.NORM_EXTERNAL &&
+          clone.normalized_reads != undefined &&
+          clone.normalized_reads[time] != null &&
+          raw == undefined) {
+              return clone.normalized_reads[time] ;
       } else {
         return clone.reads[time] ;
       }

browser/test/QUnit/testFiles/clone_test.js

@@ -119,7 +119,7 @@ var json_clone6 = {
         "id" : "id6",
         "germline" : "TRG",
         "reads" : [10,10,0,30],
-        "normalized_reads" : [20,20,0,30],
+        "normalized_reads" : [20,20,0,null],
     }
 
 QUnit.test("name, informations, getHtmlInfo", function(assert) {

browser/test/QUnit/testFiles/model_test.js

@@ -423,6 +423,12 @@ QUnit.test("normalization", function(assert) {
     m.initClones()
     assert.equal(m.have_external_normalization, false, "Model have_external_normalization is correctly resetted")
 
+
+    m.set_normalization(m.NORM_EXTERNAL)
+    assert.equal(m.normalize_reads(c6, 0, undefined), 20, "normalize_reads; get normalized value if present")
+    assert.equal(m.normalize_reads(c6, 0, false),     10, "normalize_reads; get raw value if specified" )
+    assert.equal(m.normalize_reads(c6, 2, undefined),  0, "normalize_reads; get value at 0 as computed by external normalization" )
+    assert.equal(m.normalize_reads(c6, 3, undefined), 30, "normalize_reads; get raw value if normalization equal null")
 })
 
 QUnit.test("findGermlineFromGene", function(assert) {

tools/fuse.py

@@ -317,10 +317,11 @@ class ListWindows(VidjilJson):
 
         for clone in self:
             for i, s in enumerate(clone.d["reads"]):
-                for r in range(len(ranges)):
-                    if s*1. / self.d['reads'].d['segmented'][i] >= ranges[r]:
-                        break 
-                result[r][i] += s
+                if self.d['reads'].d['segmented'][i] > 0:
+                    for r in range(len(ranges)):
+                        if s*1. / self.d['reads'].d['segmented'][i] >= ranges[r]:
+                            break
+                    result[r][i] += s
                 
         for r in range(len(ranges)):
             ratio_in_string = '{0:.10f}'.format(ranges[r]).rstrip('0')

tools/tests/should-get-tests/fuse-normalized_reads.should-get

+!LAUNCH: python ../../fuse.py $FUSE_OPTIONS ../../../algo/tests/data/no_clones.vidjil ../../../algo/tests/data/results-two-clones-1-2.vidjil -o normalized_zero.vidjil; cat normalized_zero.vidjil
+
+$ Case zero; No field normalized_reads if not contain in the given files/clones
+0: normalized_reads
+
+
+!LAUNCH: python ../../fuse.py $FUSE_OPTIONS ../../../algo/tests/data/results-two-clones-1-3.vidjil ../../../algo/tests/data/results-two-clones-1-3.vidjil -o normalized_both.vidjil; cat normalized_both.vidjil
+
+$ Case both; Should find 1 field normalized_reads (clone id-1)
+1: normalized_reads
+
+$ Case both; Correct fusion of normalized_reads field if both clones are informatives
+lr: normalized_reads.*500,.*500
+
+
+
+!LAUNCH: python ../../fuse.py $FUSE_OPTIONS ../../../algo/tests/data/no_clones.vidjil ../../../algo/tests/data/results-two-clones-1-3.vidjil -o normalized_one.vidjil; cat normalized_one.vidjil
+
+$ Case only one; Should find 1 filed normalized_reads
+1: normalized_reads
+
+$ Case only one; First value is null if on of file have not been annalysed by the normalization script
+1: null
+rl1: normalized_reads.*null,.*500
+
+
+
+!LAUNCH: python ../../fuse.py $FUSE_OPTIONS ../../../algo/tests/data/results-two-clones-1-3.vidjil ../../../algo/tests/data/no_clones.vidjil -o normalized_one_revert.vidjil; cat normalized_one_revert.vidjil
+
+$ Case inverse; Should find 1 filed normalized_reads
+1: normalized_reads
+
+$ Case inverse; Idem, but reverse files
+1: null
+lr: "normalized_reads".*500,.*null
+
+
+
+!LAUNCH: python ../../fuse.py $FUSE_OPTIONS normalized_one.vidjil ../../../algo/tests/data/results-two-clones-1-3.vidjil -o normalized_double.vidjil; cat normalized_double.vidjil
+$ Case double timepoint; Should find 1 filed normalized_reads
+1: normalized_reads
+
+$ Case double timepoint; Correct fusion if one of the file is a already fused vidjil
+1: null
+lr: "normalized_reads".*null,.*500,.*500
\ No newline at end of file

tools/utils.py

@@ -52,8 +52,13 @@ def concatenate_with_padding(d,
             continue
 
         d[key] = d1[key]
-        if key not in d2 :
-            d[key] += t2
+        ### For field normalized_reads, we prefer set it at None if not available for a timepoint
+        # Create a specific loop for it
+        if key not in d2:
+            if key != "normalized_reads":
+                d[key] += t2
+            elif key == "normalized_reads":
+                d[key] += [None]*len(d2["reads"])
 
     for key in d2:
         if key in ignore_keys:
@@ -61,8 +66,11 @@ def concatenate_with_padding(d,
         if type(d2[key]) is not list:
             continue
 
-        if key not in d :
-            d[key] = t1 + d2[key]
+        if key not in d:
+            if key != "normalized_reads":
+                d[key] = t1 + d2[key]
+            elif key == "normalized_reads":
+                d[key] = [None]*len(d1["reads"]) + d2[key]
         else :
             d[key] = d[key] + d2[key]