@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 2.24.0 → 2.25.0

package/.turbo/turbo-build.log

@@ -1,6 +1,6 @@
  WARN  Issue while reading "/home/runner/work/mixcr-clonotyping/mixcr-clonotyping/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
 
-> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.24.0 build /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.25.0 build /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
 > rm -rf dist && pl-tengo check && pl-tengo build
 
   info: Skipping unknown file type: test/columns.test.ts

package/CHANGELOG.md

@@ -1,5 +1,11 @@
 # @platforma-open/milaboratories.mixcr-clonotyping.workflow
 
+## 2.25.0
+
+### Minor Changes
+
+- 427ffa6: Include junction lengths and total number of added nt
+
 ## 2.24.0
 
 ### Minor Changes

package/dist/tengo/lib/calculate-export-specs.lib.tengo

@@ -541,6 +541,52 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 	}
 
 
+	junctionTypes := [ "VJ", "VD", "DJ" ]
+	for junctionType in junctionTypes {
+		feature := junctionType + "Junction"
+		naRegex := junctionType == "VJ" ? "region_not_covered" : "no_d_gene"
+		
+		columnsSpecPerClonotypeNoAggregates += [ {
+			column: "nLength" + feature,
+			id: "n-length-" + text.to_lower(junctionType) + "-junction",
+			naRegex: naRegex,
+			allowNA: true,
+			spec: {
+				name: "pl7.app/vdj/sequenceLength",
+				valueType: "Int",
+				domain: {
+					"pl7.app/vdj/feature": feature,
+					"pl7.app/alphabet": "nucleotide"
+				},
+				annotations: a(orderP, false, {
+					"pl7.app/label": "Length of " + junctionType + " Junction nt"
+				})
+			}
+		} ]
+		exportArgs += [ [ "-nLength", feature ] ]
+		orderP -= 100
+	}
+	
+
+	columnsSpecPerClonotypeNoAggregates += [ {
+		column: "nLengthTotalAdded",
+		id: "n-length-total-added",
+		naRegex: "region_not_covered|no_d_gene",
+		allowNA: true,
+		spec: {
+			name: "pl7.app/vdj/sequenceLength",
+			valueType: "Int",
+			domain: {
+				"pl7.app/alphabet": "nucleotide"
+			},
+			annotations: a(orderP, false, {
+				"pl7.app/label": "Total number of added nt"
+			})
+		}
+	} ]
+	orderP -= 100
+
+
 
 	geneHitColumnVariants := [ {
 			name: "pl7.app/vdj/geneHitWithAllele",

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-clonotyping-2.workflow",
-  "version": "2.24.0",
+  "version": "2.25.0",
   "description": "Tengo-based template",
   "dependencies": {
     "@platforma-sdk/workflow-tengo": "^4.10.0",

package/src/aggregate-by-clonotype-key.tpl.tengo

@@ -75,7 +75,7 @@ self.body(func(inputs) {
 	aggExpressions := []
 
 	for colDef in schemaPerClonotypeNoAggregates {
-		if colDef.column == "clonotypeLabel" {
+		if colDef.column == "clonotypeLabel" || colDef.column == "nLengthTotalAdded" {
 			continue
 		}
 		aggExpressions = append(aggExpressions,
@@ -91,6 +91,14 @@ self.body(func(inputs) {
 
 	aggregatedDf := currentDf.groupBy("clonotypeKey").agg(aggExpressions...)
 
+	// Calculate total added nucleotides: VDJunction + DJJunction for chains with D genes, VJJunction for chains without D genes
+	aggregatedDf = aggregatedDf.withColumns(
+		pt.when(pt.col("nLengthVDJunction").isNotNull().and(pt.col("nLengthVDJunction").neq("no_d_gene"))).
+			then(pt.col("nLengthVDJunction").cast("Int").plus(pt.col("nLengthDJJunction").cast("Int"))).
+			otherwise(pt.col("nLengthVJJunction").cast("Int")).
+			alias("nLengthTotalAdded")
+	)
+
 	aggregatedDf = clonotypeLabel.addClonotypeLabelColumnsPt(aggregatedDf, "clonotypeKey", "clonotypeLabel", pt)
 
 	aggregatedDf.save("output.tsv")

package/src/calculate-export-specs.lib.tengo

@@ -540,6 +540,52 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 		}
 	}
 
+	// Include junction lengths for calculation of total added nucleotides
+	junctionTypes := [ "VJ", "VD", "DJ" ]
+	for junctionType in junctionTypes {
+		feature := junctionType + "Junction"
+		naRegex := junctionType == "VJ" ? "region_not_covered" : "no_d_gene"
+		
+		columnsSpecPerClonotypeNoAggregates += [ {
+			column: "nLength" + feature,
+			id: "n-length-" + text.to_lower(junctionType) + "-junction",
+			naRegex: naRegex,
+			allowNA: true,
+			spec: {
+				name: "pl7.app/vdj/sequenceLength",
+				valueType: "Int",
+				domain: {
+					"pl7.app/vdj/feature": feature,
+					"pl7.app/alphabet": "nucleotide"
+				},
+				annotations: a(orderP, false, {
+					"pl7.app/label": "Length of " + junctionType + " Junction nt"
+				})
+			}
+		} ]
+		exportArgs += [ [ "-nLength", feature ] ]
+		orderP -= 100
+	}
+	
+	// Spec for total added length (calculated by pt in aggregate-by-clonotype-key, no flag)
+	columnsSpecPerClonotypeNoAggregates += [ {
+		column: "nLengthTotalAdded",
+		id: "n-length-total-added",
+		naRegex: "region_not_covered|no_d_gene",
+		allowNA: true,
+		spec: {
+			name: "pl7.app/vdj/sequenceLength",
+			valueType: "Int",
+			domain: {
+				"pl7.app/alphabet": "nucleotide"
+			},
+			annotations: a(orderP, false, {
+				"pl7.app/label": "Total number of added nt"
+			})
+		}
+	} ]
+	orderP -= 100
+
 	// VDJC Hits
 
 	geneHitColumnVariants := [ {