@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 2.15.0 → 2.16.0

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@2.15.0 build /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.16.0 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/.turbo/turbo-test.log

@@ -1,21 +1,21 @@
  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@2.15.0 test /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.16.0 test /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
 > vitest
 
 
  RUN  v2.1.8 /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
 
- ✓ src/test/columns.test.ts (6 tests) 52445ms
-   ✓ checking preset for 'milab-human-dna-xcr-7genes-multiplex' 12503ms
-   ✓ checking preset for '10x-sc-xcr-vdj' 8220ms
-   ✓ checking preset for 'cellecta-human-rna-xcr-umi-drivermap-…' 8387ms
-   ✓ checking preset for 'takara-human-rna-bcr-umi-smartseq' 8138ms
-   ✓ checking preset for 'rna-seq' 7510ms
-   ✓ checking preset for 'generic-single-cell-gex' 7686ms
+ ✓ src/test/columns.test.ts (6 tests) 52032ms
+   ✓ checking preset for 'milab-human-dna-xcr-7genes-multiplex' 12517ms
+   ✓ checking preset for '10x-sc-xcr-vdj' 7966ms
+   ✓ checking preset for 'cellecta-human-rna-xcr-umi-drivermap-…' 7939ms
+   ✓ checking preset for 'takara-human-rna-bcr-umi-smartseq' 8375ms
+   ✓ checking preset for 'rna-seq' 7527ms
+   ✓ checking preset for 'generic-single-cell-gex' 7706ms
 
  Test Files  1 passed (1)
       Tests  6 passed (6)
-   Start at  14:46:56
-   Duration  53.25s (transform 43ms, setup 0ms, collect 570ms, tests 52.44s, environment 0ms, prepare 69ms)
+   Start at  20:31:27
+   Duration  52.90s (transform 57ms, setup 0ms, collect 619ms, tests 52.03s, environment 0ms, prepare 68ms)
 

package/CHANGELOG.md

@@ -1,5 +1,17 @@
 # @platforma-open/milaboratories.mixcr-clonotyping.workflow
 
+## 2.16.0
+
+### Minor Changes
+
+- 632c7c0: fixed bugs with assemblingFeature and updated ptransform to 1.4.0
+
+## 2.15.1
+
+### Patch Changes
+
+- 1c2dc52: Add --force-overwrite option to avoid rare bug
+
 ## 2.15.0
 
 ### Minor Changes

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

@@ -36,24 +36,30 @@ assemblingFeatureInfo := func(assemblingFeature) {
 	productiveFeature := undefined
 	coreVFeature := undefined
 	coreJFeature := undefined
-	if assemblingFeature == "CDR3" || is_undefined(assemblingFeature) {
-		productiveFeature = "CDR3"
-	} else if assemblingFeature == "VDJRegion" {
-		productiveFeature = "VDJRegion(0,-1)"
-		coreVFeature = "{FR1Begin:FR3End}"
-		coreJFeature = "FR4"
-	} else {
-		splittedFeature := text.split(assemblingFeature, "_TO_")
-		if len(splittedFeature) == 2 {
-			if splittedFeature[1] == "FR4" {
-				productiveFeature = splittedFeature[0] + "_TO_FR4(0,-1)"
-				coreVFeature = "{"+splittedFeature[0]+"Begin:FR3End}"
+	if assemblingFeature {
+		splittedFeature1 := text.split(assemblingFeature, "_TO_")
+		splittedFeature2 := text.split(assemblingFeature, ":")
+		if assemblingFeature == "CDR3" {
+			productiveFeature = "CDR3"
+		} else if assemblingFeature == "VDJRegion" {
+			productiveFeature = "VDJRegion(0,-1)"
+			coreVFeature = "{FR1Begin:FR3End}"
+			coreJFeature = "FR4"
+		} else if len(splittedFeature1) == 2 {
+			if splittedFeature1[1] == "FR4" {
+				productiveFeature = splittedFeature1[0] + "_TO_FR4(0,-1)"
+				coreVFeature = "{"+splittedFeature1[0]+"Begin:FR3End}"
 				coreJFeature = "FR4"
 			} else {
 				productiveFeature = assemblingFeature
-				coreVFeature = "{"+splittedFeature[0]+"Begin:FR3End}"
+				coreVFeature = "{"+splittedFeature1[0]+"Begin:FR3End}"
 			}
+		} else if len(splittedFeature2) == 2 {
+			productiveFeature = assemblingFeature
+			coreVFeature = splittedFeature2[0]+":FR3End}"
 		}
+	} else {
+		productiveFeature = "CDR3"
 	}
 	return {
 		productiveFeature: productiveFeature,
@@ -64,6 +70,14 @@ assemblingFeatureInfo := func(assemblingFeature) {
 	}
 }
 
+
+formatId := func(input) {
+    noNums := text.re_replace(`\(\s*-?\d+(\s*,\s*-?\d+)*\s*\)`, input, "")
+    noBraces := text.re_replace(`[{}\(\)]`, noNums, "")
+    result   := text.re_replace(`:`, noBraces, "-")
+    return result
+}
+
 exportSpecOpsFromPreset := func(presetSpecForBack) {
 	assemblingFeature := undefined
 	if !is_undefined(presetSpecForBack.assemblingFeature) {
@@ -302,7 +316,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 		imputedU := isImputed ? "Imputed" : ""
 		imputedL := text.to_lower(imputedU)
 		for featureU in features {
-			featureL := text.to_lower(featureU)
+			featureL := text.to_lower(formatId(featureU))
 			for isAminoAcid in [true, false] {
 				alphabet := isAminoAcid ? "aminoacid" : "nucleotide"
 				alphabetShort := isAminoAcid ? "aa" : "nt"

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-clonotyping-2.workflow",
-  "version": "2.15.0",
+  "version": "2.16.0",
   "description": "Tengo-based template",
   "dependencies": {
     "@platforma-sdk/workflow-tengo": "^4.1.2",
@@ -10,7 +10,7 @@
   "devDependencies": {
     "@platforma-sdk/tengo-builder": "^2.1.0",
     "@platforma-open/milaboratories.software-mixcr": "4.7.0-165-develop",
-    "@platforma-open/milaboratories.software-ptransform": "^1.3.1",
+    "@platforma-open/milaboratories.software-ptransform": "^1.4.0",
     "@platforma-sdk/test": "^1.29.17",
     "vitest": "~2.1.8",
     "typescript": "~5.5.4"

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

@@ -36,24 +36,30 @@ assemblingFeatureInfo := func(assemblingFeature) {
 	productiveFeature := undefined
 	coreVFeature := undefined
 	coreJFeature := undefined
-	if assemblingFeature == "CDR3" || is_undefined(assemblingFeature) {
-		productiveFeature = "CDR3"
-	} else if assemblingFeature == "VDJRegion" {
-		productiveFeature = "VDJRegion(0,-1)"
-		coreVFeature = "{FR1Begin:FR3End}"
-		coreJFeature = "FR4"
-	} else {
-		splittedFeature := text.split(assemblingFeature, "_TO_")
-		if len(splittedFeature) == 2 {
-			if splittedFeature[1] == "FR4" {
-				productiveFeature = splittedFeature[0] + "_TO_FR4(0,-1)"
-				coreVFeature = "{"+splittedFeature[0]+"Begin:FR3End}"
+	if assemblingFeature {
+		splittedFeature1 := text.split(assemblingFeature, "_TO_")
+		splittedFeature2 := text.split(assemblingFeature, ":")
+		if assemblingFeature == "CDR3" {
+			productiveFeature = "CDR3"
+		} else if assemblingFeature == "VDJRegion" {
+			productiveFeature = "VDJRegion(0,-1)"
+			coreVFeature = "{FR1Begin:FR3End}"
+			coreJFeature = "FR4"
+		} else if len(splittedFeature1) == 2 {
+			if splittedFeature1[1] == "FR4" {
+				productiveFeature = splittedFeature1[0] + "_TO_FR4(0,-1)"
+				coreVFeature = "{"+splittedFeature1[0]+"Begin:FR3End}"
 				coreJFeature = "FR4"
 			} else {
 				productiveFeature = assemblingFeature
-				coreVFeature = "{"+splittedFeature[0]+"Begin:FR3End}"
+				coreVFeature = "{"+splittedFeature1[0]+"Begin:FR3End}"
 			}
+		} else if len(splittedFeature2) == 2 {
+			productiveFeature = assemblingFeature
+			coreVFeature = splittedFeature2[0]+":FR3End}"
 		}
+	} else {
+		productiveFeature = "CDR3"
 	}
 	return {
 		productiveFeature: productiveFeature,
@@ -64,6 +70,14 @@ assemblingFeatureInfo := func(assemblingFeature) {
 	}
 }
 
+// sometimes we need to format assembling feature to be used in column ids
+formatId := func(input) {
+    noNums := text.re_replace(`\(\s*-?\d+(\s*,\s*-?\d+)*\s*\)`, input, "")
+    noBraces := text.re_replace(`[{}\(\)]`, noNums, "")
+    result   := text.re_replace(`:`, noBraces, "-")
+    return result
+}
+
 exportSpecOpsFromPreset := func(presetSpecForBack) {
 	assemblingFeature := undefined
 	if !is_undefined(presetSpecForBack.assemblingFeature) {
@@ -302,7 +316,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 		imputedU := isImputed ? "Imputed" : ""
 		imputedL := text.to_lower(imputedU)
 		for featureU in features {
-			featureL := text.to_lower(featureU)
+			featureL := text.to_lower(formatId(featureU))
 			for isAminoAcid in [true, false] {
 				alphabet := isAminoAcid ? "aminoacid" : "nucleotide"
 				alphabetShort := isAminoAcid ? "aa" : "nt"

package/src/mixcr-analyze.tpl.tengo

@@ -143,6 +143,7 @@ self.body(func(inputs) {
 	}
 
 	mixcrCmdBuilder.arg("result")
+	mixcrCmdBuilder.arg("--force-overwrite")
 
 	mixcrCmdBuilder.saveFile("result.qc.json")
 	mixcrCmdBuilder.saveFile(clnsFileName)