moving back to upperchase Chr

Clinical-Genomics · Nov 13, 2020 · 4baf128 · 4baf128
1 parent 404dd03
commit 4baf128
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Showing 5 changed files with 13 additions and 13 deletions.
diff --git a/NIPTool/models/constants.py b/NIPTool/models/constants.py
@@ -25,11 +25,11 @@
     "Chr10_Ratio",
     "Chr11_Ratio",
     "Chr12_Ratio",
-    "chr13_Ratio",
-    "chr18_Ratio",
-    "chr21_Ratio",
-    "chrX_Ratio",
-    "chrY_Ratio",
+    "Chr13_Ratio",
+    "Chr18_Ratio",
+    "Chr21_Ratio",
+    "ChrX_Ratio",
+    "ChrY_Ratio",
     "Chr14_Ratio",
     "Chr15_Ratio",
     "Chr16_Ratio",

diff --git a/NIPTool/models/validation.py b/NIPTool/models/validation.py
@@ -48,10 +48,10 @@
     "Zscore_18",
     "Zscore_21",
     "Zscore_X",
-    "chr13_Ratio",
-    "chr18_Ratio",
-    "chr21_Ratio",
-    "chrX_Ratio",
+    "Chr13_Ratio",
+    "Chr18_Ratio",
+    "Chr21_Ratio",
+    "ChrX_Ratio",
     "Chr1_Ratio",
     "Chr2_Ratio",
     "Chr3_Ratio",
@@ -71,7 +71,7 @@
     "Chr19_Ratio",
     "Chr20_Ratio",
     "Chr22_Ratio",
-    "chrY_Ratio",
+    "ChrY_Ratio",
     "Median_13",
     "Median_18",
     "Median_21",

diff --git a/NIPTool/server/templates/batch/header.html b/NIPTool/server/templates/batch/header.html
@@ -4,7 +4,7 @@
 
 <div class="vertical-center">
     <div class="row">
-        <div class="col-lg-9"><h1>Batch: {{batch.SampleProject}}</h1></div>
+        <div class="col-lg-9"><h1>Batch: {{batch._id}}</h1></div>
         <div class="col-lg-3"></div>
     </div>
     <div class="row">

diff --git a/NIPTool/server/views.py b/NIPTool/server/views.py
@@ -43,7 +43,7 @@ def statistics():
 
     nr_batches = 3
     scatter_plots = ['Stdev_13', 'Stdev_18', 'Stdev_21']
-    box_plots = ['chr13_Ratio', 'chr18_Ratio', 'chr21_Ratio','FF_Formatted', 
+    box_plots = ['Chr13_Ratio', 'Chr18_Ratio', 'Chr21_Ratio','FF_Formatted', 
                 'DuplicationRate', 'MappedReads', 'GC_Dropout']
 
     batches = get_last_batches(adapter=app.adapter, nr=nr_batches)

diff --git a/tests/fixtures/valid_fluffy.csv b/tests/fixtures/valid_fluffy.csv
@@ -1,4 +1,4 @@
-"SampleID","SampleType","SequencingDate","Flowcell","SampleProject","Index1","Index2","Library_nM","QCFlag","Zscore_13","Zscore_18","Zscore_21","Zscore_X","chr13_Ratio","chr18_Ratio","chr21_Ratio","chrX_Ratio","Chr1_Ratio","Chr2_Ratio","Chr3_Ratio","Chr4_Ratio","Chr5_Ratio","Chr6_Ratio","Chr7_Ratio","Chr8_Ratio","Chr9_Ratio","Chr10_Ratio","Chr11_Ratio","Chr12_Ratio","Chr14_Ratio","Chr15_Ratio","Chr16_Ratio","Chr17_Ratio","Chr19_Ratio","Chr20_Ratio","Chr22_Ratio","chrY_Ratio","MappedReads","Chr1","Chr2","Chr3","Chr4","Chr5","Chr6","Chr7","Chr8","Chr9","Chr10","Chr11","Chr12","Chr13","Chr14","Chr15","Chr16","Chr17","Chr18","Chr19","Chr20","Chr21","Chr22","ChrX","ChrY","Median_13","Median_18","Median_21","Median_X","Median_Y","Stdev_13","Stdev_18","Stdev_21","Stdev_X","Stdev_Y","FF_Formatted","FFY","FFX","DuplicationRate","GC_Dropout","AT_Dropout","Bin2BinVariance","UnfilteredCNVcalls","CNVSegment"
+"SampleID","SampleType","SequencingDate","Flowcell","SampleProject","Index1","Index2","Library_nM","QCFlag","Zscore_13","Zscore_18","Zscore_21","Zscore_X","Chr13_Ratio","Chr18_Ratio","Chr21_Ratio","ChrX_Ratio","Chr1_Ratio","Chr2_Ratio","Chr3_Ratio","Chr4_Ratio","Chr5_Ratio","Chr6_Ratio","Chr7_Ratio","Chr8_Ratio","Chr9_Ratio","Chr10_Ratio","Chr11_Ratio","Chr12_Ratio","Chr14_Ratio","Chr15_Ratio","Chr16_Ratio","Chr17_Ratio","Chr19_Ratio","Chr20_Ratio","Chr22_Ratio","ChrY_Ratio","MappedReads","Chr1","Chr2","Chr3","Chr4","Chr5","Chr6","Chr7","Chr8","Chr9","Chr10","Chr11","Chr12","Chr13","Chr14","Chr15","Chr16","Chr17","Chr18","Chr19","Chr20","Chr21","Chr22","ChrX","ChrY","Median_13","Median_18","Median_21","Median_X","Median_Y","Stdev_13","Stdev_18","Stdev_21","Stdev_X","Stdev_Y","FF_Formatted","FFY","FFX","DuplicationRate","GC_Dropout","AT_Dropout","Bin2BinVariance","UnfilteredCNVcalls","CNVSegment"
 "s1","","","","201862","CAGGTTCC","CGAACACC","","","1.5664573178018133","5.793500349195296","-0.03448465688921887","-22.44843877490911","1.00392976488","1.0145378044","0.999592517988","0.895534547566","0.995645196832","0.993212778561","0.962823087616","1.06202342547","0.99049923318","1.00919569724","1.03740345147","0.98228215486","0.980352236205","0.990497684064","0.961517632949","1.01303209758","0.986809900603","0.995026518647","0.996175293127","1.03451169241","1.04821216494","0.95282466333","1.04782507766","0.0001070592771502772","29208118","2029934","1858430","1420819","1157784","1259965","1230164","1245957","1088639","967314","1175662","1072024","1072024","626410","735444","748838","876563","935427","569534","745983","662560","297366","486441","1010813","3127","0.994623404680424","1.0195054713461809","1.0071055241565698","0.8408228472301729","0.00010440296512402996","0.014076824975766818","0.00951751006008498","0.0067511745446958305","0.02980007629378627","6.950867669456978e-05","exist.","0.0","","0.1005291748","0.000012","33.401583","0.025028197511760338","48","Found"
 "s2","","","","201862","TTACCTGG","ACGATTGC","","","1.3836664736113866","5.81331308777849","3.7073462327488547","-35.56898088560138","1.00345380527","1.01458753978","1.01449670237","0.834596652286","0.990601777174","0.995167604367","0.962072961919","1.05777118464","0.993385479259","1.01240316831","1.03903325686","0.991366632222","0.983488534995","0.993293317385","0.95505612457","1.01314923931","0.973499284889","0.991858047435","0.988736547703","1.03613747718","1.05346928988","0.947528223568","1.03829176495","0.00018379807248525016","19619357","1354513","1243481","947437","772255","840547","827926","833468","730865","648361","787219","716799","716799","419651","486482","500012","580410","626225","378761","503768","442069","201359","324729","645131","3606","0.994623404680424","1.0195054713461809","1.0071055241565698","0.8408228472301729","0.00010440296512402996","0.014076824975766818","0.00951751006008498","0.0067511745446958305","0.02980007629378627","6.950867669456978e-05","exist.","4.61122090143","","0.103652428568","0.000187","33.815994","0.022890283030606213","45","Found"
 "s3","","","","201862","CTATCATT","GACCACCT","","","1.197714750470135","5.993678160991702","0.1722130673672542","-27.33721401871472","1.00296961522","1.01504030531","1.00041582109","0.872828803296","0.994369406522","0.994050565447","0.963985487377","1.06586994","0.991903746769","1.01417054338","1.04011435706","0.989841130219","0.987191423231","0.990561923283","0.952624100278","1.01511372968","0.975874349841","0.997388670577","0.996128439123","1.04577514591","1.06297625217","0.947324666538","1.04127965945","0.00010174665309778273","30035386","2011620","1827738","1395600","1133559","1235029","1212946","1232408","1076087","965009","1163613","1060576","1060576","617068","723824","745525","876814","949260","556232","772443","660420","298174","492289","980817","3056","0.994623404680424","1.0195054713461809","1.0071055241565698","0.8408228472301729","0.00010440296512402996","0.014076824975766818","0.00951751006008498","0.0067511745446958305","0.02980007629378627","6.950867669456978e-05","exist.","0.0","","0.100858034586","0.000097","34.339258","0.026603482197962082","40","Found"