@platforma-open/milaboratories.mixcr-shm-trees.workflow 3.2.1 → 3.3.0

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Files changed (10) hide show
  1. package/.turbo/turbo-build.log +1 -1
  2. package/CHANGELOG.md +6 -0
  3. package/dist/tengo/lib/soi-export.lib.tengo +40 -6
  4. package/dist/tengo/tpl/main.plj.gz +0 -0
  5. package/dist/tengo/tpl/process.plj.gz +0 -0
  6. package/dist/tengo/tpl/reconstruct-shm-trees.plj.gz +0 -0
  7. package/dist/tengo/tpl/soi.plj.gz +0 -0
  8. package/package.json +5 -5
  9. package/src/soi-export.lib.tengo +40 -6
  10. package/src/soi.tpl.tengo +54 -1
package/.turbo/turbo-build.log CHANGED
@@ -1,5 +1,5 @@
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1
 
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- > @platforma-open/milaboratories.mixcr-shm-trees.workflow@3.2.1 build /home/runner/work/mixcr-shm-trees/mixcr-shm-trees/workflow
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+ > @platforma-open/milaboratories.mixcr-shm-trees.workflow@3.3.0 build /home/runner/work/mixcr-shm-trees/mixcr-shm-trees/workflow
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  > rm -rf dist && pl-tengo check && pl-tengo build
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4
 
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  Processing "src/export-settings.lib.tengo"...
package/CHANGELOG.md CHANGED
@@ -1,5 +1,11 @@
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  # @platforma-open/milaboratories.mixcr-shm-trees.workflow
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+ ## 3.3.0
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+
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+ ### Minor Changes
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+
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+ - b8c818f: Alignment-based sequence search for sequence collections, multiple other improvements for this subsystem
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+
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  ## 3.2.1
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10
 
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  ### Patch Changes
package/dist/tengo/lib/soi-export.lib.tengo CHANGED
@@ -1,6 +1,9 @@
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  ll := import("@platforma-sdk/workflow-tengo:ll")
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2
 
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  soiResultImportColumns := func(dbParameters) {
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+ commonDomain := {
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+ "pl7.app/list": dbParameters.id
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+ }
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  if dbParameters.searchParameters.type == "tree_search_top" {
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  return [ {
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  column: "topHit",
@@ -12,9 +15,7 @@ soiResultImportColumns := func(dbParameters) {
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  "pl7.app/label": "Top Hit " + dbParameters.name
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  }
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  },
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- domain: {
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- "pl7.app/list": dbParameters.id
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- }
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+ domain: commonDomain
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  }, {
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  column: "mutations",
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  id: "mutations",
@@ -25,9 +26,42 @@ soiResultImportColumns := func(dbParameters) {
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  "pl7.app/label": "Number of mutations " + dbParameters.name
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  }
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  },
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- domain: {
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- "pl7.app/list": dbParameters.id
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- }
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+ domain: commonDomain
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+ } ]
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+ } else if dbParameters.searchParameters.type == "preset_alignment_search_top" {
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+ return [ {
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+ column: "topHit",
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+ id: "topHit",
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+ spec: {
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+ name: "pl7.app/search/topHit",
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+ valueType: "String",
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+ annotations: {
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+ "pl7.app/label": "Top Hit " + dbParameters.name
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+ }
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+ },
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+ domain: commonDomain
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+ }, {
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+ column: "penalty",
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+ id: "penalty",
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+ spec: {
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+ name: "pl7.app/search/alignmentPenalty",
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+ valueType: "Int",
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+ annotations: {
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+ "pl7.app/label": "Alignment penalty " + dbParameters.name
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+ }
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+ },
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+ domain: commonDomain
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+ }, {
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+ column: "score",
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+ id: "score",
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+ spec: {
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+ name: "pl7.app/search/alignmentScore",
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+ valueType: "Int",
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+ annotations: {
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+ "pl7.app/label": "Alignment score " + dbParameters.name
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+ }
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+ },
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+ domain: commonDomain
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  } ]
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  } else {
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  ll.panic("Unknown search mode: " + dbParameters.searchParameters.type)
package/dist/tengo/tpl/main.plj.gz CHANGED
Binary file
package/dist/tengo/tpl/process.plj.gz CHANGED
Binary file
package/dist/tengo/tpl/soi.plj.gz CHANGED
Binary file
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@platforma-open/milaboratories.mixcr-shm-trees.workflow",
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- "version": "3.2.1",
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+ "version": "3.3.0",
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  "type": "module",
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  "description": "Tengo-based template",
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  "//": {
@@ -8,13 +8,13 @@
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  },
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  "devDependencies": {
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  "@platforma-sdk/tengo-builder": "^1.17.5",
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- "@platforma-sdk/workflow-tengo": "^2.9.2",
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- "@milaboratories/software-pframes-conv": "^2.1.3",
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+ "@platforma-sdk/workflow-tengo": "^2.9.6",
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+ "@milaboratories/software-pframes-conv": "^2.1.5",
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  "@platforma-open/milaboratories.software-small-binaries": "^1.15.6",
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  "@platforma-open/milaboratories.software-mixcr": "4.7.0-139-develop",
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- "@platforma-open/milaboratories.software-mitool": "2.3.1-2-main",
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+ "@platforma-open/milaboratories.software-mitool": "2.3.1-5-main",
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  "@platforma-open/milaboratories.software-paggregate": "^1.0.1",
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- "@platforma-sdk/test": "^1.21.9",
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+ "@platforma-sdk/test": "^1.21.20",
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  "vitest": "^2.1.8",
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  "typescript": "~5.6.3"
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  },
package/src/soi-export.lib.tengo CHANGED
@@ -1,6 +1,9 @@
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  ll := import("@platforma-sdk/workflow-tengo:ll")
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  soiResultImportColumns := func(dbParameters) {
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+ commonDomain := {
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+ "pl7.app/list": dbParameters.id
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+ }
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  if dbParameters.searchParameters.type == "tree_search_top" {
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  return [ {
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  column: "topHit",
@@ -12,9 +15,7 @@ soiResultImportColumns := func(dbParameters) {
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  "pl7.app/label": "Top Hit " + dbParameters.name
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  }
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  },
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- domain: {
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- "pl7.app/list": dbParameters.id
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- }
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+ domain: commonDomain
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  }, {
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  column: "mutations",
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  id: "mutations",
@@ -25,9 +26,42 @@ soiResultImportColumns := func(dbParameters) {
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  "pl7.app/label": "Number of mutations " + dbParameters.name
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  }
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  },
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- domain: {
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- "pl7.app/list": dbParameters.id
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- }
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+ domain: commonDomain
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+ } ]
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+ } else if dbParameters.searchParameters.type == "preset_alignment_search_top" {
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+ return [ {
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+ column: "topHit",
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+ id: "topHit",
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+ spec: {
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+ name: "pl7.app/search/topHit",
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+ valueType: "String",
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+ annotations: {
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+ "pl7.app/label": "Top Hit " + dbParameters.name
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+ }
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+ },
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+ domain: commonDomain
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+ }, {
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+ column: "penalty",
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+ id: "penalty",
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+ spec: {
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+ name: "pl7.app/search/alignmentPenalty",
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+ valueType: "Int",
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+ annotations: {
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+ "pl7.app/label": "Alignment penalty " + dbParameters.name
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+ }
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+ },
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+ domain: commonDomain
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+ }, {
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+ column: "score",
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+ id: "score",
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+ spec: {
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+ name: "pl7.app/search/alignmentScore",
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+ valueType: "Int",
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+ annotations: {
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+ "pl7.app/label": "Alignment score " + dbParameters.name
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+ }
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+ },
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+ domain: commonDomain
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  } ]
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  } else {
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  ll.panic("Unknown search mode: " + dbParameters.searchParameters.type)
package/src/soi.tpl.tengo CHANGED
@@ -1,4 +1,5 @@
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  self := import("@platforma-sdk/workflow-tengo:tpl")
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+ ll := import("@platforma-sdk/workflow-tengo:ll")
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  assets := import("@platforma-sdk/workflow-tengo:assets")
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  maps := import("@platforma-sdk/workflow-tengo:maps")
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  exec := import("@platforma-sdk/workflow-tengo:exec")
@@ -74,6 +75,58 @@ self.body(func(inputs) {
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  inputTsv := xsv.exportFrame([{spec: modifiedQuerySpec, data: queryData}], "tsv", {})
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+ actualSearchParameters := db.parameters.searchParameters
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+ if actualSearchParameters.type == "preset_alignment_search_top" {
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+ // nVDJRegion: 369
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+ // nCDR3: 51
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+ // aaVDJRegion: 641
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+ // aaCDR3: 93
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+ if db.parameters.type == "nucleotide" {
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+ actualSearchParameters = {
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+ type: "banded_alignment_search_top",
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+ scoring: {
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+ match: 1,
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+ mismatch: -2,
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+ gap: {
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+ type: "affine",
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+ openPenalty: -3,
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+ extensionPenalty: -1
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+ }
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+ },
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+ band: 9
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+ }
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+ if db.parameters.targetFeature == "CDR3" {
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+ actualSearchParameters.maxPenalty = 1 + int(51 * db.parameters.searchParameters.dissimilarityPercent / 100)
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+ } else if db.parameters.targetFeature == "VDJRegion" {
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+ actualSearchParameters.maxPenalty = 1 + int(369 * db.parameters.searchParameters.dissimilarityPercent / 100)
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+ } else {
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+ ll.panic("Unknown target feature: " + db.parameters.targetFeature)
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+ }
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+ } else if db.parameters.type == "amino-acid" {
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+ actualSearchParameters = {
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+ type: "banded_alignment_search_top",
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+ scoring: {
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+ matrix: "BLOSUM62",
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+ gap: {
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+ type: "affine",
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+ openPenalty: -10,
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+ extensionPenalty: -1
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+ }
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+ },
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+ band: 4
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+ }
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+ if db.parameters.targetFeature == "CDR3" {
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+ actualSearchParameters.maxPenalty = 1 + int(93 * db.parameters.searchParameters.dissimilarityPercent / 100)
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+ } else if db.parameters.targetFeature == "VDJRegion" {
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+ actualSearchParameters.maxPenalty = 1 + int(641 * db.parameters.searchParameters.dissimilarityPercent / 100)
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+ } else {
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+ ll.panic("Unknown target feature: " + db.parameters.targetFeature)
124
+ }
125
+ } else {
126
+ ll.panic("Unknown alphabet: " + db.parameters.type)
127
+ }
128
+ }
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+
77
130
  searchCmd := exec.builder().
78
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  printErrStreamToStdout().
79
132
  secret("MI_LICENSE", "MI_LICENSE").
@@ -83,7 +136,7 @@ self.body(func(inputs) {
83
136
  arg("--database").arg("database.tsv").
84
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  writeFile("database.tsv", dbData).
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  arg("--parameters").arg("params.json").
86
- writeFile("params.json", json.encode(db.parameters.searchParameters)).
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+ writeFile("params.json", json.encode(actualSearchParameters)).
87
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  arg("--hits-only").
88
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  arg("--target-column").arg("query").
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  arg("input.tsv").addFile("input.tsv", inputTsv).