diff --git a/.changeset/purple-snakes-stop.md b/.changeset/purple-snakes-stop.md new file mode 100644 index 0000000..d4c0ced --- /dev/null +++ b/.changeset/purple-snakes-stop.md @@ -0,0 +1,16 @@ +--- +"@platforma-open/milaboratories.generation-probability.software": major +"@platforma-open/milaboratories.generation-probability.workflow": major +"@platforma-open/milaboratories.generation-probability.block": major +"@platforma-open/milaboratories.generation-probability.model": major +"@platforma-open/milaboratories.generation-probability.ui": major +--- + +Initial release. + +- Per-clonotype generation probability (Pgen) via OLGA on BCR and TCR + repertoires from MiXCR clonotyping. +- Human and mouse models for IGH, IGK, IGL, TRA, and TRB; recombination + model resolved from dataset species and per-chain locus metadata. +- Emits raw Pgen and -log10(Pgen) per chain (heavy/light for BCR, + beta/alpha for TCR). diff --git a/block/docs/description.md b/block/docs/description.md new file mode 100644 index 0000000..aeb7b15 --- /dev/null +++ b/block/docs/description.md @@ -0,0 +1,13 @@ +# Overview + +For every clonotype in a repertoire, this block computes the chance that V(D)J recombination would build its exact CDR3 by chance, before any immune selection — a value called its generation probability (Pgen). Some CDR3s form readily through many recombination paths (high Pgen); others sit far from the sequences recombination favors and are rare (low Pgen). Pgen spans about twenty orders of magnitude across a repertoire, so it ranks clonotypes on a scale that V/J gene usage and clone abundance cannot. + +What a rare CDR3 means depends on your data. In post-immunisation antibody (BCR) repertoires, a rare heavy-chain CDR3 has drifted far from germline through affinity maturation, so Pgen ranks lead candidates by that distance. T-cell (TCR) repertoires undergo no somatic hypermutation, so there Pgen instead separates common public CDR3s — shared across people by chance — from rare, clonally expanded ones. + +Each clonotype carries the raw Pgen and its −log10 form, where a higher −log10 marks a rarer CDR3, computed on its primary chain. These values feed downstream ranking blocks such as Lead Selection. + +# Method + +Pgen is computed with [OLGA](https://github.com/statbiophys/OLGA) v1.3.0, which sums over the V(D)J recombination paths that yield each CDR3 under a learned model. Calibrated models cover human and mouse across IGH / IGK / IGL / TRA / TRB. On anything else — another species such as camelid, or sequences with no true V(D)J origin such as display libraries and synthetic sets — OLGA still returns a number, but one with no biological meaning. OLGA is distributed under GPL-3.0. + +> Sethna Z, Elhanati Y, Callan CG Jr, Walczak AM, Mora T. OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs. _Bioinformatics_ 35(17):2974–2981, 2019. [doi:10.1093/bioinformatics/btz035](https://doi.org/10.1093/bioinformatics/btz035) diff --git a/block/package.json b/block/package.json index 904ddcd..35a54e3 100644 --- a/block/package.json +++ b/block/package.json @@ -41,12 +41,22 @@ "ui": "@platforma-open/milaboratories.generation-probability.ui/dist" }, "meta": { - "title": "generation-probability", - "description": "generation-probability block", + "title": "Generation Probability", "logo": "file:logos/block-logo.png", + "url": "https://github.com/platforma-open/generation-probability", + "support": "mailto:support@milaboratories.com", + "description": "Scores each BCR or TCR clonotype by how likely V(D)J recombination is to produce its CDR3 by chance — its generation probability (Pgen) — a clonal-rarity and germline-distance signal for lead ranking.", + "longDescription": "file:docs/description.md", + "changelog": "file:CHANGELOG.md", + "tags": [ + "vdj", + "bcr", + "tcr", + "downstream" + ], "organization": { - "name": "milaboratories", - "url": "https://example.com", + "name": "MiLaboratories Inc", + "url": "https://milaboratories.com/", "logo": "file:logos/organization-logo.png" } } diff --git a/model/package.json b/model/package.json index 0fcb2d9..a557dc3 100644 --- a/model/package.json +++ b/model/package.json @@ -21,6 +21,8 @@ "check": "ts-builder check --target block-model" }, "dependencies": { + "@milaboratories/graph-maker": "catalog:", + "@milaboratories/helpers": "catalog:", "@platforma-sdk/model": "catalog:" }, "devDependencies": { diff --git a/model/src/index.ts b/model/src/index.ts index 3e9bc4c..a07feff 100644 --- a/model/src/index.ts +++ b/model/src/index.ts @@ -1,13 +1,183 @@ -import type { InferOutputsType } from "@platforma-sdk/model"; -import { BlockModelV3, DataModelBuilder } from "@platforma-sdk/model"; +import type { GraphMakerState } from "@milaboratories/graph-maker"; +import { + AccessorColumnsProvider, + BlockModelV3, + ColumnsCollection, + createPFrameForGraphs, + createPlDataTableStateV2, + createPlDataTableV3, + DataModelBuilder, + deriveColumnOptions, + InferOutputsType, + ListOptionBase, + PColumn, + PColumnDataUniversal, + PColumnIdAndSpec, + PlDataTableStateV2, +} from "@platforma-sdk/model"; -export type BlockArgs = Record; +export const SPECIES_OPTIONS = [ + { label: "Human", value: "human" }, + { label: "Mouse", value: "mouse" }, +] as const; -const dataModel = new DataModelBuilder().from("v1").init(() => ({})); +export const PGEN_NAME = "pl7.app/vdj/generationProbability"; +const CHAIN_NAME = "pl7.app/vdj/chain"; + +export type BlockData = { + inputAnchor?: string; + datasetLabel: string; + species?: (typeof SPECIES_OPTIONS)[number]["value"]; + tableState: PlDataTableStateV2; + distributionGraphState: GraphMakerState; +}; + +const inputSelectors = [ + { + axes: [{ name: "pl7.app/vdj/clonotypeKey" }], + annotations: { "pl7.app/isAnchor": "true" }, + }, + { + axes: [{ name: "pl7.app/vdj/scClonotypeKey" }], + annotations: { "pl7.app/isAnchor": "true" }, + }, + { + axes: [{ name: "pl7.app/variantKey" }], + annotations: { "pl7.app/isAnchor": "true" }, + }, +]; + +const dataModel = new DataModelBuilder().from("v1").init(() => ({ + datasetLabel: "", + tableState: createPlDataTableStateV2(), + distributionGraphState: { + title: "Generation Probability", + template: "bins", + currentTab: null, + layersSettings: { bins: { fillColor: "#99E099" } }, + axesSettings: { axisY: { scale: "log" } }, + }, +})); export const platforma = BlockModelV3.create(dataModel) - .args(() => ({})) - .sections(() => [{ type: "link", href: "/", label: "Main" }]) + + .args((data) => { + if (data.inputAnchor == null) throw new Error("Input dataset is required"); + if (data.species == null) throw new Error("Species is required"); + return { + inputAnchor: data.inputAnchor, + species: data.species, + }; + }) + + .output("inputOptions", () => { + const collection = ColumnsCollection(["result_pool"]).filter({ + include: inputSelectors, + }); + const scorableIds = new Set( + collection + .getColumns() + .filter( + (anchor) => + !ColumnsCollection(["result_pool"]) + .discover({ + anchors: { main: anchor.getSpec() }, + include: [{ name: [{ type: "exact", value: CHAIN_NAME }] }], + mode: "enrichment", + }) + .isEmpty(), + ) + .map((anchor) => anchor.id), + ); + return deriveColumnOptions(collection) + .filter(({ id }) => scorableIds.has(id)) + .map>(({ id, label }) => ({ value: id, label })); + }) + + .outputWithStatus("pgenTable", (ctx) => { + const pgenOutput = ctx.outputs?.resolve("pgenPf"); + if (pgenOutput === undefined) return undefined; + const collection = ColumnsCollection([pgenOutput]); + if (!collection.isFinal()) return undefined; + return createPlDataTableV3(ctx, { + primaryColumns: collection.filter({ include: [{ name: PGEN_NAME }] }).getColumns(), + columns: collection.filter({ exclude: [{ name: PGEN_NAME }] }).getColumns(), + tableState: ctx.data.tableState, + }); + }) + + // Only the raw pgen columns (one per chain), so the graph's value picker doubles as the + // Heavy/Light chooser. + .outputWithStatus("pgenGraphPf", (ctx) => { + const pgenOutput = ctx.outputs?.resolve("pgenPf"); + if (pgenOutput === undefined) return undefined; + const provider = AccessorColumnsProvider(pgenOutput); + if (!provider.isFinal()) return undefined; + const pgenCols = provider + .getColumns() + .map>((column) => ({ + id: column.id, + spec: column.getSpec(), + data: column.getData(), + })) + .filter((column) => column.spec.name === PGEN_NAME); + if (pgenCols.length === 0) return undefined; + return createPFrameForGraphs(ctx, pgenCols); + }) + + .output("pgenGraphPfCols", (ctx) => { + const pgenOutput = ctx.outputs?.resolve("pgenPf"); + if (pgenOutput === undefined) return undefined; + const provider = AccessorColumnsProvider(pgenOutput); + if (!provider.isFinal()) return undefined; + return provider + .getColumns() + .map((column) => ({ columnId: column.id, spec: column.getSpec() })) + .filter((column) => column.spec.name === PGEN_NAME); + }) + + .output("progress", (ctx) => + ctx.outputs + ?.resolve("progress") + ?.getProgressLog("progress: ") + .mapDefined((progressLine) => { + const progress = progressLine?.match(/progress: (?\S+)/)?.groups?.progress; + if (!progress) return true; + return Number(progress) || true; + }), + ) + + .output("skippedChains", (ctx) => + ctx.outputs + ?.resolve("progress") + ?.getProgressLog("skipped: ") + .mapDefined((line) => { + const match = line?.match(/skipped: (?.*)/)?.groups; + if (!match) return undefined; + const chains = match.chains.split(",").filter(Boolean); + if (chains.length === 0) return undefined; + return chains; + }), + ) + + .output("isRunning", (ctx) => ctx.outputs?.getIsReadyOrError() === false) + + .title(() => "Generation Probability") + + .subtitle((ctx) => + [ + ctx.data.datasetLabel, + SPECIES_OPTIONS.find((option) => option.value === ctx.data.species)?.label, + ] + .filter(Boolean) + .join(" - "), + ) + + .sections(() => [ + { type: "link", href: "/", label: "Main" }, + { type: "link", href: "/distribution", label: "Distribution" }, + ]) + .done(); export type BlockOutputs = InferOutputsType; diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml index 04ce84d..91790f8 100644 --- a/pnpm-lock.yaml +++ b/pnpm-lock.yaml @@ -9,6 +9,12 @@ catalogs: '@changesets/cli': specifier: ~2.29.8 version: 2.29.8 + '@milaboratories/graph-maker': + specifier: 1.6.1 + version: 1.6.1 + '@milaboratories/helpers': + specifier: 1.14.5 + version: 1.14.5 '@milaboratories/ts-builder': specifier: 1.6.1 version: 1.6.1 @@ -111,6 +117,12 @@ importers: model: dependencies: + '@milaboratories/graph-maker': + specifier: 'catalog:' + version: 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'@typescript/typescript-darwin-x64@7.0.2': + optional: true + + '@typescript/typescript-freebsd-arm64@7.0.2': + optional: true + + '@typescript/typescript-freebsd-x64@7.0.2': + optional: true + + '@typescript/typescript-linux-arm64@7.0.2': + optional: true + + '@typescript/typescript-linux-arm@7.0.2': + optional: true + + '@typescript/typescript-linux-loong64@7.0.2': + optional: true + + '@typescript/typescript-linux-mips64el@7.0.2': + optional: true + + '@typescript/typescript-linux-ppc64@7.0.2': + optional: true + + '@typescript/typescript-linux-riscv64@7.0.2': + optional: true + + '@typescript/typescript-linux-s390x@7.0.2': + optional: true + + '@typescript/typescript-linux-x64@7.0.2': + optional: true + + '@typescript/typescript-netbsd-arm64@7.0.2': + optional: true '@typescript/typescript-netbsd-x64@7.0.2': optional: true @@ -8044,6 +12409,8 @@ snapshots: ag-charts-locale@12.1.2: optional: true + ag-charts-types@10.3.9: {} + ag-charts-types@12.1.2: {} ag-grid-community@34.1.2: @@ -8351,6 +12718,8 @@ snapshots: colorette@1.4.0: {} + comlink@4.4.2: {} + commander@10.0.1: {} commander@14.0.3: {} @@ -8423,12 +12792,36 @@ snapshots: d3-color@3.1.0: {} + d3-dispatch@3.0.1: {} + + d3-drag@3.0.0: + dependencies: + d3-dispatch: 3.0.1 + d3-selection: 3.0.0 + + d3-ease@3.0.1: {} + d3-format@3.1.2: {} + d3-hierarchy@3.1.2: {} + d3-interpolate@3.0.1: dependencies: d3-color: 3.1.0 + d3-path@3.1.0: {} + + d3-polygon@3.0.1: {} + + d3-quadtree@3.0.1: {} + + d3-random@3.0.1: {} + + d3-scale-chromatic@3.1.0: + dependencies: + d3-color: 3.1.0 + d3-interpolate: 3.0.1 + d3-scale@4.0.2: dependencies: d3-array: 3.2.4 @@ -8439,6 +12832,10 @@ snapshots: d3-selection@3.0.0: {} + d3-shape@3.2.0: + dependencies: + d3-path: 3.1.0 + d3-time-format@4.1.0: dependencies: d3-time: 3.1.0 @@ -8447,8 +12844,31 @@ snapshots: dependencies: d3-array: 3.2.4 + d3-timer@3.0.1: {} + + d3-transition@3.0.1(d3-selection@3.0.0): + dependencies: + d3-color: 3.1.0 + d3-dispatch: 3.0.1 + d3-ease: 3.0.1 + d3-interpolate: 3.0.1 + d3-selection: 3.0.0 + d3-timer: 3.0.1 + + d3-zoom@3.0.0: + dependencies: + d3-dispatch: 3.0.1 + d3-drag: 3.0.0 + d3-interpolate: 3.0.1 + d3-selection: 3.0.0 + d3-transition: 3.0.1(d3-selection@3.0.0) + de-indent@1.0.2: {} + debug@2.6.9: + dependencies: + ms: 2.0.0 + debug@4.4.3: dependencies: ms: 2.1.3 @@ -8962,6 +13382,8 @@ snapshots: optionalDependencies: graceful-fs: 4.2.11 + kdbush@4.1.0: {} + kolorist@1.8.0: {} kuler@2.0.0: {} @@ -9128,6 +13550,8 @@ snapshots: mri@1.2.0: {} + ms@2.0.0: {} + ms@2.1.3: {} muggle-string@0.4.1: {} @@ -9439,6 +13863,12 @@ snapshots: '@jitl/quickjs-wasmfile-release-sync': 0.31.0 quickjs-emscripten-core: 0.31.0 + quickselect@3.0.0: {} + + rbush@4.0.1: + dependencies: + quickselect: 3.0.0 + rc@1.2.8: dependencies: deep-extend: 0.6.0 @@ -9446,6 +13876,13 @@ snapshots: minimist: 1.2.8 strip-json-comments: 2.0.1 + react-dom@19.2.8(react@19.2.8): + dependencies: + react: 19.2.8 + scheduler: 0.27.0 + + react@19.2.8: {} + read-yaml-file@1.1.0: dependencies: graceful-fs: 4.2.11 @@ -9623,6 +14060,8 @@ snapshots: safer-buffer@2.1.2: {} + scheduler@0.27.0: {} + seek-bzip@1.0.6: dependencies: commander: 2.20.3 diff --git a/pnpm-workspace.yaml b/pnpm-workspace.yaml index 65449cc..6d53f82 100644 --- a/pnpm-workspace.yaml +++ b/pnpm-workspace.yaml @@ -6,20 +6,21 @@ packages: - ui - workflow catalog: - "@platforma-sdk/model": 1.80.10 - "@platforma-sdk/ui-vue": 1.80.10 - "@platforma-sdk/workflow-tengo": 6.8.2 - "@platforma-sdk/test": 1.80.11 - "@platforma-sdk/block-tools": 2.12.9 - "@platforma-sdk/tengo-builder": 4.0.20 - "@platforma-sdk/package-builder": 3.14.2 + "@changesets/cli": ~2.29.8 + "@milaboratories/graph-maker": 1.6.1 + "@milaboratories/helpers": 1.14.5 "@milaboratories/ts-builder": 1.6.1 "@milaboratories/ts-configs": 1.3.1 - turbo: ~2.8.11 - shx: ~0.4.0 - "@changesets/cli": ~2.29.8 - vitest: ~4.0.18 "@platforma-open/milaboratories.runenv-python-3": 1.8.2 - vue: 3.5.24 - "@milaboratories/helpers": 1.14.5 - typescript: 7.0.2 + "@platforma-sdk/block-tools": 2.12.9 + "@platforma-sdk/model": 1.80.10 + "@platforma-sdk/package-builder": 3.14.2 + "@platforma-sdk/tengo-builder": 4.0.20 + "@platforma-sdk/test": 1.80.11 + "@platforma-sdk/ui-vue": 1.80.10 + "@platforma-sdk/workflow-tengo": 6.8.2 + "shx": ~0.4.0 + "turbo": ~2.8.11 + "typescript": "7.0.2" + "vitest": ~4.0.18 + "vue": 3.5.24 diff --git a/software/.python-version b/software/.python-version new file mode 100644 index 0000000..e4fba21 --- /dev/null +++ b/software/.python-version @@ -0,0 +1 @@ +3.12 diff --git a/software/package.json b/software/package.json index d1586b4..1fa2b20 100644 --- a/software/package.json +++ b/software/package.json @@ -10,7 +10,8 @@ "build": "block-tools software build", "do-pack": "shx rm -f *.tgz && block-tools software build && pnpm pack && shx mv platforma-open*.tgz package.tgz", "changeset": "changeset", - "version-packages": "changeset version" + "version-packages": "changeset version", + "deps:export": "bash scripts/deps-export.sh" }, "devDependencies": { "@platforma-open/milaboratories.runenv-python-3": "catalog:", diff --git a/software/pyproject.toml b/software/pyproject.toml new file mode 100644 index 0000000..5b7f240 --- /dev/null +++ b/software/pyproject.toml @@ -0,0 +1,20 @@ +[project] +name = "software" +version = "0.1.0" +description = "Add your description here" +readme = "README.md" +requires-python = ">=3.12" +dependencies = [ + "olga>=1.3.0", + "polars[rtcompat]>=1.43.0", +] + +[dependency-groups] +dev = [ + "ruff>=0.16.0", + "ty>=0.0.63", +] + +[tool.ruff.lint] +select = ["ALL"] +ignore = ["CPY", "D", "T20"] diff --git a/software/scripts/deps-export.sh b/software/scripts/deps-export.sh new file mode 100644 index 0000000..530a58a --- /dev/null +++ b/software/scripts/deps-export.sh @@ -0,0 +1,11 @@ +#!/usr/bin/env bash +# Regenerate src/requirements.txt from pyproject.toml (the single source of truth). +# One definition, shared by `pnpm deps:export` and the requirements-sync CI job. +# +# --no-deps: top-level pins only. The scientific-slim runenv supplies transitive +# deps for the offline (--no-index) install, so requirements.txt must not pin a +# full closure. +set -euo pipefail +cd "$(dirname "$0")/.." +uv pip compile pyproject.toml \ + --custom-compile-command "pnpm deps:export" -o src/requirements.txt diff --git a/software/src/main.py b/software/src/main.py index 90d42d2..420ff61 100644 --- a/software/src/main.py +++ b/software/src/main.py @@ -1,3 +1,238 @@ +import multiprocessing +import os import sys +import threading +from argparse import ArgumentParser +from concurrent.futures import ProcessPoolExecutor +from dataclasses import dataclass +from enum import Enum +from functools import cache, partial +from pathlib import Path -print("Hello from Python, " + sys.argv[1] + "!") +import polars as pl +from olga import generation_probability, load_model +from olga.performance.fast_pgen import FastPgen + + +class Alphabet(Enum): + AMINO_ACID = "aminoacid" + NUCLEOTIDE = "nucleotide" + + +class Species(Enum): + HUMAN = "human" + MOUSE = "mouse" + + +class Recombination(Enum): + VDJ = "VDJ" + VJ = "VJ" + + +CHAIN_MODELS = { + "IGH": ("B_heavy", Recombination.VDJ), + "IGK": ("B_kappa", Recombination.VJ), + "IGL": ("B_lambda", Recombination.VJ), + "TRB": ("T_beta", Recombination.VDJ), + "TRA": ("T_alpha", Recombination.VJ), +} + + +@dataclass(frozen=True, slots=True) +class Args: + input: Path + output: Path + species: Species + alphabet: Alphabet + key_column: str + sequence_columns: list[str] + chain_columns: list[str] + pgen_columns: list[str] + neg_log_pgen_columns: list[str] + workers: int + + +@cache +def get_model(chain: str, species: Species) -> FastPgen | None: + try: + name, recombination = CHAIN_MODELS[chain] + except KeyError: + return None + base = ( + Path(load_model.__file__).parent / "default_models" / f"{species.value}_{name}" + ) + match recombination: + case Recombination.VDJ: + genomic = load_model.GenomicDataVDJ() + generative = load_model.GenerativeModelVDJ() + model_init = generation_probability.GenerationProbabilityVDJ + case Recombination.VJ: + genomic = load_model.GenomicDataVJ() + generative = load_model.GenerativeModelVJ() + model_init = generation_probability.GenerationProbabilityVJ + genomic.load_igor_genomic_data( + base / "model_params.txt", + base / "V_gene_CDR3_anchors.csv", + base / "J_gene_CDR3_anchors.csv", + ) + generative.load_and_process_igor_model(base / "model_marginals.txt") + return FastPgen(model_init(generative, genomic)) + + +def compute_pgen( + sequence: str, + chain: str, + alphabet: Alphabet, + species: Species, +) -> float | None: + model = get_model(chain, species) + if not model: + return None + match alphabet: + case Alphabet.AMINO_ACID: + compute = model.compute_aa_CDR3_pgen + case Alphabet.NUCLEOTIDE: + compute = model.compute_nt_CDR3_pgen + return compute(sequence, print_warnings=False) + + +def parse_args() -> Args: + parser = ArgumentParser() + parser.add_argument("--input", required=True, type=Path) + parser.add_argument("--output", required=True, type=Path) + parser.add_argument("--species", required=True, type=Species) + parser.add_argument("--alphabet", required=True, type=Alphabet) + parser.add_argument("--key-column", required=True) + parser.add_argument( + "--sequence-column", + required=True, + action="append", + dest="sequence_columns", + ) + parser.add_argument( + "--chain-column", + required=True, + action="append", + dest="chain_columns", + ) + parser.add_argument( + "--pgen-column", + required=True, + action="append", + dest="pgen_columns", + ) + parser.add_argument( + "--neg-log-pgen-column", + required=True, + action="append", + dest="neg_log_pgen_columns", + ) + parser.add_argument("--workers", type=int, default=os.cpu_count() or 1) + return Args(**vars(parser.parse_args())) + + +def main() -> None: + args = parse_args() + df = pl.scan_parquet(args.input) + + columns = set(df.collect_schema().names()) + missing_columns = { + args.key_column, + *args.sequence_columns, + *args.chain_columns, + } - columns + if missing_columns: + msg = f"columns not found in {args.input}: {missing_columns}" + raise SystemExit(msg) + if args.workers < 1: + msg = f"--workers must be >= 1, got {args.workers}" + raise SystemExit(msg) + if len(args.sequence_columns) != len(args.chain_columns): + msg = ( + "number of sequence columns and chain columns do not match " + f"({len(args.sequence_columns)} ≠ {len(args.chain_columns)})" + ) + raise SystemExit(msg) + + total = df.select(pl.len()).collect().item() * len(args.sequence_columns) + supported_chains = set(CHAIN_MODELS) + + score = partial(compute_pgen, alphabet=args.alphabet, species=args.species) + + progress_lock = threading.Lock() + done = 0 + skipped_chains: set[str] = set() + + with ProcessPoolExecutor( + max_workers=args.workers, + mp_context=multiprocessing.get_context("forkserver"), + ) as pool: + + def process_batch(batch: pl.Series) -> pl.Series: + nonlocal done + chains = batch.struct.field("chain") + result = pl.Series( + pool.map( + score, + batch.struct.field("sequence"), + chains, + chunksize=len(batch) // args.workers or 1, + ), + ) + with progress_lock: + done += int(batch.struct.field("multiplicity").sum()) + skipped_chains.update( + chain + for chain in chains + if chain is not None and chain not in supported_chains + ) + progress = min(1, done / total if total else 1) + print(f"progress: {progress:.3f}", file=sys.stderr) + return result + + res = df + + for sequence, chain, pgen, neg_log_pgen in zip( + args.sequence_columns, + args.chain_columns, + args.pgen_columns, + args.neg_log_pgen_columns, + strict=True, + ): + multiplicity = "multiplicity" + while multiplicity in (sequence, chain): + multiplicity = "_" + multiplicity + distinct = ( + df.select(sequence, chain) + .drop_nulls() + .group_by(sequence, chain) + .len(name=multiplicity) + ) + pgen_col = ( + pl.struct(sequence=sequence, chain=chain, multiplicity=multiplicity) + .map_batches( + process_batch, + return_dtype=pl.Float64, + is_elementwise=True, + ) + .alias(pgen) + ) + scored = ( + distinct.with_columns(pgen_col) + .with_columns(-pl.col(pgen).log10().alias(neg_log_pgen)) + .select(sequence, chain, pgen, neg_log_pgen) + ) + res = res.join(scored, on=(sequence, chain), how="left") + + res.select( + args.key_column, + *args.pgen_columns, + *args.neg_log_pgen_columns, + ).sink_parquet(args.output, engine="streaming") + + if skipped_chains: + print(f"skipped: {','.join(sorted(skipped_chains))}", file=sys.stderr) + + +if __name__ == "__main__": + main() diff --git a/software/src/requirements.txt b/software/src/requirements.txt index 9b0bd8e..4e7679d 100644 --- a/software/src/requirements.txt +++ b/software/src/requirements.txt @@ -1 +1,18 @@ -# No dependencies specified for this script +# This file was autogenerated by uv via the following command: +# pnpm deps:export +llvmlite==0.48.0 + # via numba +numba==0.66.0 + # via 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-11,7 +11,9 @@ "check": "ts-builder check --target block-ui" }, "dependencies": { + "@milaboratories/graph-maker": "catalog:", "@platforma-open/milaboratories.generation-probability.model": "workspace:*", + "@platforma-sdk/model": "catalog:", "@platforma-sdk/ui-vue": "catalog:", "vue": "catalog:" }, diff --git a/ui/src/MainPage.vue b/ui/src/MainPage.vue deleted file mode 100644 index 93e842f..0000000 --- a/ui/src/MainPage.vue +++ /dev/null @@ -1,9 +0,0 @@ - - - diff --git a/ui/src/app.ts b/ui/src/app.ts index 98849f8..9f4fd5a 100644 --- a/ui/src/app.ts +++ b/ui/src/app.ts @@ -1,10 +1,16 @@ import { platforma } from "@platforma-open/milaboratories.generation-probability.model"; import { defineAppV3 } from "@platforma-sdk/ui-vue"; -import MainPage from "./MainPage.vue"; +import DistributionPage from "./pages/DistributionPage.vue"; +import MainPage from "./pages/MainPage.vue"; -export const sdkPlugin = defineAppV3(platforma, () => ({ +export const sdkPlugin = defineAppV3(platforma, (app) => ({ + progress: () => { + if (!app.model.outputs.isRunning) return undefined; + return app.model.outputs.progress ?? true; + }, routes: { "/": () => MainPage, + "/distribution": () => DistributionPage, }, })); diff --git a/ui/src/main.ts b/ui/src/main.ts index cef5df0..899885c 100644 --- a/ui/src/main.ts +++ b/ui/src/main.ts @@ -1,5 +1,5 @@ +import { BlockLayout } from "@platforma-sdk/ui-vue"; import { createApp } from "vue"; import { sdkPlugin } from "./app"; -import { BlockLayout } from "@platforma-sdk/ui-vue"; createApp(BlockLayout).use(sdkPlugin).mount("#app"); diff --git a/ui/src/pages/DistributionPage.vue b/ui/src/pages/DistributionPage.vue new file mode 100644 index 0000000..d783988 --- /dev/null +++ b/ui/src/pages/DistributionPage.vue @@ -0,0 +1,37 @@ + + + diff --git a/ui/src/pages/MainPage.vue b/ui/src/pages/MainPage.vue new file mode 100644 index 0000000..3833312 --- /dev/null +++ b/ui/src/pages/MainPage.vue @@ -0,0 +1,78 @@ + + + diff --git a/workflow/src/main.tpl.tengo b/workflow/src/main.tpl.tengo index 6eeeee1..ed696e6 100644 --- a/workflow/src/main.tpl.tengo +++ b/workflow/src/main.tpl.tengo @@ -1,10 +1,105 @@ -// Workflow entry point for generation-probability. - wf := import("@platforma-sdk/workflow-tengo:workflow") +render := import("@platforma-sdk/workflow-tengo:render") +assets := import("@platforma-sdk/workflow-tengo:assets") +ll := import("@platforma-sdk/workflow-tengo:ll") +json := import("json") + +scoreTpl := assets.importTemplate(":score") + +ENTITY_KEY_NAMES := { + "pl7.app/vdj/clonotypeKey": true, + "pl7.app/vdj/scClonotypeKey": true, + "pl7.app/variantKey": true +} + +// The alphabet may live directly on the key axis domain, or nested in the structured +// key's `/structure` domain under the CDR3 sequence entry. +alphabetFromStructure := func(structureStr) { + if is_undefined(structureStr) { + return undefined + } + for entry in json.decode(structureStr) { + if len(entry) == 0 || entry[0] != "pl7.app/vdj/sequence" { + continue + } + for idx, item in entry { + if idx > 0 && item[0] == "pl7.app/alphabet" { + return item[1] + } + } + } + return undefined +} + +// Resolve only the anchor spec here; CDR3/chain columns are resolved in the child (score), +// which anchors them by the entity-key axis name — unknown until the anchor spec resolves. +wf.prepare(func(args) { + bundleBuilder := wf.createPBundleBuilder() + bundleBuilder.ignoreMissingDomains() + bundleBuilder.addAnchor("main", json.decode(args.inputAnchor)) + return { + columns: bundleBuilder.build() + } +}) wf.body(func(args) { - return { - outputs: {}, - exports: {} - } + anchorRef := json.decode(args.inputAnchor) + datasetSpec := args.columns.getSpec(anchorRef) + + keySpec := undefined + for axis in datasetSpec.axesSpec { + if !is_undefined(ENTITY_KEY_NAMES[axis.name]) { + keySpec = axis + break + } + } + if is_undefined(keySpec) { + ll.panic("Selected dataset has no clonotype or variant key axis") + } + + keyDomain := is_undefined(keySpec.domain) ? {} : keySpec.domain + alphabet := keyDomain["pl7.app/alphabet"] + if is_undefined(alphabet) { + alphabet = alphabetFromStructure(keyDomain[keySpec.name + "/structure"]) + } + if is_undefined(alphabet) { + ll.panic("Cannot determine CDR3 alphabet") + } + + // Forward only trace + label, so an unrelated datasetSpec change doesn't bust the + // downstream cache. + datasetLabel := "" + traceAnnotations := {} + if !is_undefined(datasetSpec.annotations) { + if !is_undefined(datasetSpec.annotations["pl7.app/label"]) { + datasetLabel = datasetSpec.annotations["pl7.app/label"] + } + if !is_undefined(datasetSpec.annotations["pl7.app/trace"]) { + traceAnnotations = { "pl7.app/trace": datasetSpec.annotations["pl7.app/trace"] } + } + } + + scoreResult := render.createEphemeral(scoreTpl, { + ctx: wf.getParentBCtx(), + anchorRef: anchorRef, + keyName: keySpec.name, + keySpec: keySpec, + alphabet: alphabet, + species: args.species, + datasetLabel: datasetLabel, + traceAnnotations: traceAnnotations + }) + + // Retention TTL: keeps this expensive result warm so an identical re-request within a + // day is recovered instead of recomputed. + cacheMillis := 24 * 60 * 60 * 1000 + return { + outputs: { + pgenPf: scoreResult.output("pgenPf", cacheMillis), + progress: scoreResult.output("progress", cacheMillis) + }, + exports: { + pgenPf: scoreResult.output("exportPf", cacheMillis) + } + } }) diff --git a/workflow/src/pgen-process.tpl.tengo b/workflow/src/pgen-process.tpl.tengo new file mode 100644 index 0000000..7af8828 --- /dev/null +++ b/workflow/src/pgen-process.tpl.tengo @@ -0,0 +1,121 @@ +self := import("@platforma-sdk/workflow-tengo:tpl") +exec := import("@platforma-sdk/workflow-tengo:exec") +f := import("@platforma-sdk/workflow-tengo:exec.formula") +assets := import("@platforma-sdk/workflow-tengo:assets") +pframes := import("@platforma-sdk/workflow-tengo:pframes") +pSpec := import("@platforma-sdk/workflow-tengo:pframes.spec") +xsv := import("@platforma-sdk/workflow-tengo:pframes.xsv") + +pgenSw := assets.importSoftware("@platforma-open/milaboratories.generation-probability.software:main") + +self.defineOutputs("pgenPf", "exportPf", "progress") + +self.body(func(args) { + params := args.params + units := params.units + + cmd := exec.builder(). + software(pgenSw). + addFile("input.parquet", args.inputTable, { tag: "input" }). + arg("--input").arg("input.parquet"). + arg("--output").arg("result.parquet"). + arg("--species").arg(params.species). + arg("--alphabet").arg(params.alphabet). + arg("--key-column").arg("clonotypeKey") + for unit in units { + cmd = cmd.arg("--sequence-column").arg("cdr3_" + unit.suffix) + cmd = cmd.arg("--chain-column").arg("chain_" + unit.suffix) + cmd = cmd.arg("--pgen-column").arg("pgen_" + unit.suffix) + cmd = cmd.arg("--neg-log-pgen-column").arg("neglog_" + unit.suffix) + } + cmd = cmd.arg("--workers").argExpr("{system.cpu}") + + // Resources scale with input parquet size (bytes track clonotype count): CPU ~ 1 core/MiB + // clamped [2, 16]; RAM ~ 4x input (decompressed strings + ~130 MB/worker) clamped [4, 32] + // GiB. Static fallbacks cover backends that can't evaluate formulas. + run := cmd. + saveFile("result.parquet"). + saveStderrStream(). + resources({ + queue: "heavy", + onCPU: { + cpu: f.size("input").dividedBy(f.mib(1)).between(2, 16).staticFallback(8), + ram: f.size("input").times(4).between(f.gib(4), f.gib(32)).staticFallback(f.gib(8)) + } + }). + run() + + resultTable := run.getFile("result.parquet") + + trace := pSpec.makeTrace({ annotations: params.traceAnnotations }, { + type: "milaboratories.generation-probability", + importance: 30, + label: "Generation Probability" + }) + + columnSpecs := [] + orderedIds := [] + for unit in units { + pgenId := "pgen_" + unit.suffix + negId := "neglog_" + unit.suffix + + labelSuffix := "" + if !is_undefined(unit.label) && unit.label != "" { + labelSuffix = " (" + unit.label + ")" + } + + columnSpecs += [{ + column: pgenId, + id: pgenId, + allowNA: true, + spec: { + name: "pl7.app/vdj/generationProbability", + valueType: "Double", + domain: unit.domain, + annotations: { + "pl7.app/label": "Generation probability" + labelSuffix, + "pl7.app/format": ".2e" + } + } + }, { + column: negId, + id: negId, + allowNA: true, + spec: { + name: "pl7.app/vdj/minlog10GenerationProbability", + valueType: "Double", + domain: unit.domain, + annotations: { + "pl7.app/label": "-log10 generation probability" + labelSuffix, + "pl7.app/format": ".2f" + } + } + }] + orderedIds += [pgenId, negId] + } + + imported := xsv.importFile(resultTable, "parquet", { + axes: [{ column: "clonotypeKey", spec: params.keySpec }], + columns: columnSpecs, + storageFormat: "Parquet", + partitionKeyLength: 0 + }, { splitDataAndSpec: true, cpu: 1, mem: "4GiB" }) + + outputBuilder := pframes.pFrameBuilder() + exportBuilder := pframes.pFrameBuilder() + for id in orderedIds { + column := imported[id] + outputBuilder.add(id, column.spec, column.data) + exportBuilder.add(id, trace.inject(column.spec), column.data) + } + + for seqId, seqSpec in params.seqSpecs { + outputBuilder.add(seqId, seqSpec, args["seqData_" + seqId]) + } + + return { + pgenPf: pframes.exportFrame(outputBuilder.build()), + exportPf: exportBuilder.build(), + progress: run.getStderrStream() + } +}) diff --git a/workflow/src/score.tpl.tengo b/workflow/src/score.tpl.tengo new file mode 100644 index 0000000..5d467ab --- /dev/null +++ b/workflow/src/score.tpl.tengo @@ -0,0 +1,199 @@ +self := import("@platforma-sdk/workflow-tengo:tpl") +render := import("@platforma-sdk/workflow-tengo:render") +smart := import("@platforma-sdk/workflow-tengo:smart") +assets := import("@platforma-sdk/workflow-tengo:assets") +pframes := import("@platforma-sdk/workflow-tengo:pframes") +pBundle := import("@platforma-sdk/workflow-tengo:pframes.bundle") + +pgenTpl := assets.importTemplate(":pgen-process") + +CHAIN_LABELS := { + "IGHeavy": "Heavy", + "IGLight": "Light", + "TCRAlpha": "Alpha", + "TCRBeta": "Beta", + "TCRGamma": "Gamma", + "TCRDelta": "Delta" +} + +SC_CHAIN_LABELS := { + "IG": { "A": "Heavy", "B": "Light" }, + "TCRAB": { "A": "Alpha", "B": "Beta" }, + "TCRGD": { "A": "Gamma", "B": "Delta" } +} + +chainLabel := func(keySpec, cdr3Col, scChain) { + if is_undefined(scChain) { + return CHAIN_LABELS[keySpec.domain["pl7.app/vdj/chain"]] + } + axis := cdr3Col.spec.axesSpec[0] + axisDomain := is_undefined(axis.domain) ? {} : axis.domain + receptor := axisDomain["pl7.app/vdj/receptor"] + if is_undefined(receptor) || is_undefined(SC_CHAIN_LABELS[receptor]) { + return undefined + } + return SC_CHAIN_LABELS[receptor][scChain] +} + +matchDomain := func(col, required) { + domain := is_undefined(col.spec.domain) ? {} : col.spec.domain + for k, v in required { + if domain[k] != v { + return false + } + } + return true +} +firstWithDomain := func(cols, required) { + for col in cols { + if matchDomain(col, required) { + return col + } + } + return undefined +} +allWithDomain := func(cols, required) { + out := [] + for col in cols { + if matchDomain(col, required) { + out += [col] + } + } + return out +} + +scSlot := func(scChain) { + return { + scChain: scChain, + chainDomain: { + "pl7.app/vdj/scClonotypeChain": scChain, + "pl7.app/vdj/scClonotypeChain/index": "primary" + } + } +} +BULK_SLOT := { scChain: undefined, chainDomain: {} } + +self.defineOutputs("pgenPf", "exportPf", "progress") + +self.prepare(func(args) { + bundleBuilder := pBundle.createBuilder(args.ctx) + bundleBuilder.ignoreMissingDomains() + bundleBuilder.addAnchor("main", args.anchorRef) + + bundleBuilder.addMulti({ + axes: [{ anchor: "main", name: args.keyName }], + name: "pl7.app/vdj/sequence", + domain: { + "pl7.app/vdj/feature": "CDR3" + } + }, "cdr3") + + bundleBuilder.addMulti({ + axes: [{ anchor: "main", name: args.keyName }], + name: "pl7.app/sequence", + domain: { + "pl7.app/feature": "CDR3" + } + }, "cdr3Plain") + + bundleBuilder.addMulti({ + axes: [{ anchor: "main", name: args.keyName }], + name: "pl7.app/vdj/chain" + }, "chain") + + return { + columns: bundleBuilder.build() + } +}) + +self.body(func(args) { + columns := args.columns + alphabet := args.alphabet + keySpec := args.keySpec + isSingleCell := keySpec.name == "pl7.app/vdj/scClonotypeKey" + + // CDR3 lives under one of two namespaces (pl7.app/vdj/sequence for clonotype keys, + // pl7.app/sequence for variantKey); merge both — only one is present, the other returns []. + cdr3Cols := columns.getColumns("cdr3") + columns.getColumns("cdr3Plain") + chainCols := columns.getColumns("chain") + + units := [] + addUnit := func(slot) { + domain := { "pl7.app/alphabet": alphabet } + for k, v in slot.chainDomain { + domain[k] = v + } + cdr3Col := firstWithDomain(cdr3Cols, domain) + chainCol := firstWithDomain(chainCols, slot.chainDomain) + if is_undefined(cdr3Col) || is_undefined(chainCol) { + return + } + units += [{ + suffix: is_undefined(slot.scChain) ? "bulk" : slot.scChain, + domain: domain, + label: chainLabel(keySpec, cdr3Col, slot.scChain), + cdr3Col: cdr3Col, + chainCol: chainCol, + seqCols: allWithDomain(cdr3Cols, slot.chainDomain) + }] + } + + slots := isSingleCell ? [scSlot("A"), scSlot("B")] : [BULK_SLOT] + for slot in slots { + addUnit(slot) + } + + // Nothing scoreable => an empty p-frame; the null progress resource makes the model + // treat the step as not-running. + if len(units) == 0 { + empty := pframes.pFrameBuilder().build() + return { + pgenPf: pframes.exportFrame(empty), + exportPf: empty, + progress: smart.createNullResource() + } + } + + tableBuilder := pframes.parquetFileBuilder() + tableBuilder.setAxisHeader(keySpec, "clonotypeKey") + unitParams := [] + for unit in units { + tableBuilder.add(unit.cdr3Col, { header: "cdr3_" + unit.suffix }) + tableBuilder.add(unit.chainCol, { header: "chain_" + unit.suffix }) + unitParams += [{ + suffix: unit.suffix, + domain: unit.domain, + label: unit.label + }] + } + tableBuilder.cpu(1) + tableBuilder.mem("4GiB") + inputTable := tableBuilder.build() + + // Specs in a keyed map so ordering can't perturb the params hash; data passed separately. + renderInputs := { inputTable: inputTable } + seqSpecs := {} + for unit in units { + for col in unit.seqCols { + seqId := "seq_" + unit.suffix + "_" + col.spec.domain["pl7.app/alphabet"] + seqSpecs[seqId] = col.spec + renderInputs["seqData_" + seqId] = col.data + } + } + renderInputs.params = smart.createJsonResource({ + species: args.species, + alphabet: alphabet, + keySpec: keySpec, + units: unitParams, + seqSpecs: seqSpecs, + datasetLabel: args.datasetLabel, + traceAnnotations: args.traceAnnotations + }) + processResult := render.create(pgenTpl, renderInputs) + + return { + pgenPf: processResult.output("pgenPf"), + exportPf: processResult.output("exportPf"), + progress: processResult.output("progress") + } +})