v2 CN/LOH (WIP): cn build-model and cn call
Cyto model (.simurg-cyto: GC 1 kb/100 kb/1 Mb, PFB from the cluster file, optional sex-aware batch reference from normal GTCs; IN-051, CYTO-038); GC-wave correction (CYTO-003); smoothing (CYTO-004); HMM with constitutional, gain-LOH, mosaic and haploid states, forward-backward QUAL and Viterbi segments (CYTO-005/012); event statistics, effective size, post-filters, per-type thresholds, promotion/LowFraction, built-in centromere mask from UCSC cytoBand (CYTO-006..021); sex resolution (CYTO-024), ploidy; CNV VCF with bgzip+tabix (CYTO-028..031), segments parquet, cn_sample_summary.tsv and the cn_call_manifest.json sidecar.
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"""``simurg cn build-model`` / ``simurg cn call`` — genome-wide CNV/LOH/mosaic calling (spec CYTO-001 … CYTO-040).
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I/O and orchestration only; the numerics live in ``simurg.cn``.
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"""
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from __future__ import annotations
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import hashlib
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import io
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import json
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import math
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import zipfile
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from dataclasses import dataclass, field
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from pathlib import Path
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from typing import Any
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import numpy as np
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import numpy.typing as npt
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import pyarrow as pa
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import pyarrow.parquet as pq
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from simurg import __version__
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from simurg.core.errors import ExitCode, SimurgError
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from simurg.core.log import Reporter
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from simurg.formats.bpm import Manifest, read_bpm
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from simurg.formats.fasta import ContigMap, Genome
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MODEL_SCHEMA = 1
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F64 = npt.NDArray[np.float64]
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def probe_set_hash(manifest: Manifest) -> str:
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h = hashlib.sha256()
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for name, chrom, pos in zip(manifest.names, manifest.chroms, manifest.map_infos.tolist(), strict=True):
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h.update(f"{name}\t{chrom}\t{pos}\n".encode())
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return h.hexdigest()
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@dataclass
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class CytoModel:
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header: dict[str, Any]
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names: list[str]
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gc: npt.NDArray[np.float32] # (n, 3): 1 kb, 100 kb, 1 Mb
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pfb: npt.NDArray[np.float32]
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ref_lrr: npt.NDArray[np.float32] | None = None # batch reference: per-probe median LRR
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ref_lrr_f: npt.NDArray[np.float32] | None = None # same, X/Y from female reference samples
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ref_lrr_m: npt.NDArray[np.float32] | None = None # same, X/Y from male reference samples
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ref_het: npt.NDArray[np.float32] | None = None # per-probe median heterozygous BAF
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def run_build_model(
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bpm: Path,
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fasta: Path,
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out: Path,
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rep: Reporter,
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egt: Path | None = None,
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contig_alias: str = "auto",
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reference_gtcs: Path | None = None,
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max_reference: int = 100,
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) -> int:
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"""CYTO-038: GC covariates (and PFB when a cluster file is given) per manifest probe → ``.simurg-cyto``."""
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from simurg.cn.model import GC_WINDOWS, gc_fractions, population_bfreq
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man = read_bpm(bpm)
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genome = Genome(fasta)
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cmap = ContigMap([e.name for e in genome.entries], contig_alias)
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chroms = np.array(man.chroms)
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pos = man.map_infos.astype(np.int64)
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gc = np.full((man.num_loci, len(GC_WINDOWS)), np.nan, dtype=np.float32)
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for chrom in sorted(set(man.chroms)):
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contig = cmap.get(chrom)
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if contig is None:
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continue
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sel = np.flatnonzero((chroms == chrom) & (pos > 0))
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if len(sel):
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gc[sel] = gc_fractions(genome._contig_array(contig), pos[sel])
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rep.info(f"GC windows for chromosome {chrom}: {len(sel)} probes")
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pfb = population_bfreq(None, man.num_loci)
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egt_name = ""
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if egt is not None:
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from simurg.formats.egt import read_egt
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from simurg.genotype.clusters import align_clusters
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clusters = align_clusters(read_egt(egt), man, allow_missing=True)
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pfb = population_bfreq(np.where(clusters.present[:, None], clusters.n, 0), man.num_loci)
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egt_name = Path(egt).name
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ref_cols: dict[str, Any] = {}
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n_ref = 0
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if reference_gtcs is not None:
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from simurg.cn.model import reference_stats
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from simurg.formats.gtc import read_gtc
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paths = sorted(reference_gtcs.rglob("*.gtc"))
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if len(paths) > max_reference:
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idx = np.random.default_rng(42).choice(len(paths), max_reference, replace=False)
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paths = [paths[i] for i in sorted(idx)]
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if len(paths) < 24:
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rep.warn("W_QC_TOO_FEW", f"batch reference from only {len(paths)} GTCs (plan: >= 24)")
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lrr = np.empty((len(paths), man.num_loci), dtype=np.float32)
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baf = np.empty((len(paths), man.num_loci), dtype=np.float32)
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sexes = []
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for i, p in enumerate(paths):
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g = read_gtc(p)
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if len(g.logr_ratios) != man.num_loci:
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raise SimurgError("E_MODEL_MANIFEST_MISMATCH", f"{p} has {len(g.logr_ratios)} loci, the manifest "
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f"{man.num_loci}") # fmt: skip
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lrr[i], baf[i] = g.logr_ratios, g.b_allele_freqs
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sexes.append(g.gender.decode(errors="replace")[:1].upper() if g.gender else "U")
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ref_lrr, ref_het, n_het = reference_stats(lrr, baf)
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# X and Y from same-sex reference samples only (CYTO-005 baselines differ by sex)
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sx = np.isin(chroms, ["X", "XY", "Y"])
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ref_by_sex = {}
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for sex in ("F", "M"):
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rows = np.array([s_ == sex for s_ in sexes])
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col = ref_lrr.copy()
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if rows.sum() >= 3:
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col[sx] = reference_stats(lrr[rows][:, sx], baf[rows][:, sx])[0]
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ref_by_sex[sex] = col
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n_f, n_m = sexes.count("F"), sexes.count("M")
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rep.info(f"batch reference sexes: {n_f} F, {n_m} M, {len(sexes) - n_f - n_m} U")
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ref_cols = {"ref_lrr": ref_lrr, "ref_lrr_f": ref_by_sex["F"], "ref_lrr_m": ref_by_sex["M"],
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"ref_het_baf": ref_het, "ref_n_het": n_het} # fmt: skip
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n_ref = len(paths)
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rep.info(f"batch reference from {n_ref} GTC(s)")
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header = {
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"schema": "simurg.cyto_model",
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"schema_version": MODEL_SCHEMA,
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"software": f"SimurgArray {__version__}",
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"manifest": man.manifest_name,
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"probe_set_sha256": probe_set_hash(man),
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"n_probes": man.num_loci,
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"genome_build": genome.build,
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"fasta_sha256": genome.sha256,
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"gc_windows_bp": list(GC_WINDOWS),
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"pfb_source": f"cluster file {egt_name}" if egt_name else "none (0.5)",
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"reference_samples": n_ref,
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}
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table = pa.table({
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"name": man.names,
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"gc_1kb": gc[:, 0], "gc_100kb": gc[:, 1], "gc_1mb": gc[:, 2],
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"pfb": pfb,
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**ref_cols,
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}) # fmt: skip
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buf = io.BytesIO()
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pq.write_table(table, buf, compression="zstd")
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out.parent.mkdir(parents=True, exist_ok=True)
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tmp = out.with_suffix(out.suffix + ".part")
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with zipfile.ZipFile(tmp, "w", compression=zipfile.ZIP_STORED) as z:
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z.writestr("header.json", json.dumps(header, indent=1))
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z.writestr("probes.parquet", buf.getvalue())
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tmp.replace(out)
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rep.info(f"cyto model for {man.num_loci} probes written to {out}")
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return ExitCode.OK
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def read_model(path: Path, manifest: Manifest) -> CytoModel:
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"""IN-051: check schema and probe set."""
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with zipfile.ZipFile(path) as z:
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header = json.loads(z.read("header.json"))
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table = pq.read_table(io.BytesIO(z.read("probes.parquet")))
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if int(header.get("schema_version", 0)) < MODEL_SCHEMA:
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raise SimurgError("E_MODEL_VERSION", f"{path}: cyto model schema {header.get('schema_version')} is too old",
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hint="rebuild it with simurg cn build-model") # fmt: skip
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if header.get("probe_set_sha256") != probe_set_hash(manifest):
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raise SimurgError("E_MODEL_MANIFEST_MISMATCH", f"{path} was built for manifest {header.get('manifest')!r}, "
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f"not {manifest.manifest_name!r} (probe set differs)") # fmt: skip
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gc = np.column_stack([table.column(c).to_numpy(zero_copy_only=False) for c in ("gc_1kb", "gc_100kb", "gc_1mb")])
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def col(c: str) -> npt.NDArray[np.float32] | None:
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return table.column(c).to_numpy(zero_copy_only=False).astype(np.float32) if c in table.column_names else None
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pfb = col("pfb")
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assert pfb is not None
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return CytoModel(header, table.column("name").to_pylist(), gc.astype(np.float32), pfb, ref_lrr=col("ref_lrr"),
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ref_lrr_f=col("ref_lrr_f"), ref_lrr_m=col("ref_lrr_m"), ref_het=col("ref_het_baf")) # fmt: skip
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# ================================================================================================ cn call
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PAR = { # 1-based inclusive pseudo-autosomal regions on X
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"GRCh38": ((10_001, 2_781_479), (155_701_383, 156_030_895)),
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"GRCh37": ((60_001, 2_699_520), (154_931_044, 155_260_560)),
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}
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CALL_CHROMS = [str(i) for i in range(1, 23)] + ["X", "Y"]
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@dataclass
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class CnCallOptions:
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out: Path
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bpm: Path
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model: Path
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gtcs: Path | None = None
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sheet: Path | None = None
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summary: Path | None = None
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fasta: Path | None = None
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thresholds: Any = None # simurg.cn.events.Thresholds
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smoothing: int = 5
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cn_cap: int = 4
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gc_correct: bool = True
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unknown_sex_policy: str = "skip-sex-chromosomes"
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gt_mode: str = "vcf"
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svlen_mode: str = "signed"
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mask_bed: Path | None = None
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bgzip: bool = True
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threads: int = 0
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force: bool = False
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argv: list[str] = field(default_factory=list)
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def _builtin_file(name: str) -> bytes:
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from importlib import resources
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return resources.files("simurg.cn").joinpath("data", name).read_bytes()
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def read_mask(path: Path | None, build: str) -> dict[str, list[tuple[int, int]]]:
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"""CYTO-017: BED (0-based half-open) → per-chromosome intervals as 1-based inclusive."""
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text = path.read_text() if path is not None else _builtin_file(f"mask_{build}.bed").decode()
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out: dict[str, list[tuple[int, int]]] = {}
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for line in text.splitlines():
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if not line.strip() or line.startswith(("#", "track", "browser")):
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continue
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c, s, e = line.split("\t")[:3]
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c = c[3:] if c.lower().startswith("chr") else c
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out.setdefault(c, []).append((int(s) + 1, int(e)))
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return out
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def moving_median(x: F64, k: int) -> F64:
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"""CYTO-004: median over 2k+1 consecutive values, truncated (never wrapped) at the ends; NaN ignored."""
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if k <= 0 or len(x) == 0:
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return x.copy()
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from numpy.lib.stride_tricks import sliding_window_view
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pad = np.concatenate([np.full(k, np.nan), x, np.full(k, np.nan)])
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with np.errstate(all="ignore"):
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import warnings
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with warnings.catch_warnings():
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warnings.simplefilter("ignore", RuntimeWarning)
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med = np.nanmedian(sliding_window_view(pad, 2 * k + 1), axis=1)
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return np.where(np.isfinite(x), med, np.nan)
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@dataclass
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class SampleInput:
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sample_id: str
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sample_name: str
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gtc: str
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sex: str # M | F | U
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logr_dev: float
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sex_source: str
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def _robust_sd(x: F64, floor: float) -> float:
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x = x[np.isfinite(x)]
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if not len(x):
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return floor
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return max(floor, float(1.4826 * np.median(np.abs(x - np.median(x)))))
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def _resolve_sex(si: SampleInput, chroms: npt.NDArray[np.str_], lrr: F64, geno: npt.NDArray[np.uint8],
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policy: str) -> tuple[str, str, list[str]]: # fmt: skip
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"""CYTO-024."""
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if si.sex in ("M", "F"):
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return si.sex, si.sex_source, []
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x = chroms == "X"
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called = geno[x] > 0
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het = float((geno[x] == 2).sum() / called.sum()) if called.any() else math.nan
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med = float(np.nanmedian(lrr[x])) if x.any() else math.nan
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if math.isfinite(het) and math.isfinite(med):
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if het < 0.03 and med < -0.15:
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return "M", "resolved", []
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if het > 0.08 and med > -0.1:
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return "F", "resolved", []
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if policy == "female":
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return "F", "assumed", ["sex_assumed"]
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if policy == "male":
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return "M", "assumed", ["sex_assumed"]
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if policy == "error":
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raise SimurgError("E_CN_SEX_UNRESOLVED", f"{si.sample_id}: sex could not be resolved")
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return "U", "unresolved", ["sex_unresolved"]
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def call_sample(si: SampleInput, ctx: dict[str, Any], opts: CnCallOptions) -> dict[str, Any]:
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"""One sample: preprocessing, per-region HMM, events, VCF + segments. Returns the summary row + events."""
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from simurg.cn import hmm
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from simurg.cn.events import (
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annotate_stats,
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apply_thresholds,
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effective_size,
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extract,
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median_spacing,
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post_filter,
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set_filters,
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)
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from simurg.cn.gcwave import gc_correct
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from simurg.formats.gtc import read_gtc
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man_chroms: npt.NDArray[np.str_] = ctx["chroms"]
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pos_all: npt.NDArray[np.int64] = ctx["pos"]
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model: CytoModel = ctx["model"]
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th = opts.thresholds
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g = read_gtc(si.gtc)
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lrr = g.logr_ratios.astype(np.float64)
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baf = g.b_allele_freqs.astype(np.float64)
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geno = g.genotypes
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lrr[~np.isfinite(lrr)] = np.nan
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baf[~np.isfinite(baf)] = np.nan
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sex, sex_source, flags = _resolve_sex(si, man_chroms, lrr - float(np.nanmedian(lrr[ctx["auto"]])), geno,
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opts.unknown_sex_policy) # fmt: skip
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ref = {"F": model.ref_lrr_f, "M": model.ref_lrr_m}.get(sex) if model.ref_lrr_f is not None else None
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if ref is None:
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ref = model.ref_lrr
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if ref is not None:
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lrr = lrr - ref
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if model.ref_het is not None:
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het = (baf > 0.1) & (baf < 0.9)
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baf = np.where(het, np.clip(baf - (model.ref_het - 0.5), 0.0, 1.0), baf)
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auto = ctx["auto"]
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gcfit = None
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if opts.gc_correct:
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lrr, gcfit = gc_correct(lrr, model.gc, auto)
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lrr = lrr - float(np.nanmedian(lrr[auto]))
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logr_dev = si.logr_dev if math.isfinite(si.logr_dev) else float(np.nanstd(lrr[auto]))
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noisy = logr_dev > 0.2
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whole_chrom_only = logr_dev > 0.3
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if noisy:
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flags.append("high_noise")
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if whole_chrom_only:
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flags.append("whole_chromosome_only")
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pfb = model.pfb.astype(np.float64)
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lrr_s = np.full_like(lrr, np.nan)
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for sel in ctx["by_chrom"].values():
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lrr_s[sel] = moving_median(lrr[sel], opts.smoothing)
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# emission SD from the unsmoothed LRR: smoothed values are autocorrelated, their own SD would overstate evidence
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seg_sd = _robust_sd(lrr[auto], 0.05)
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b_het = baf[auto & (baf > 0.3) & (baf < 0.7)]
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baf_sd = _robust_sd(b_het, 0.02)
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dip, hap = hmm.diploid_states(), hmm.haploid_states()
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counts: dict[str, int] = {}
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events: list[Any] = []
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segments: list[dict[str, Any]] = []
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ploidy_num = 0.0
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ploidy_den = 0
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par = PAR.get(ctx["build"], PAR["GRCh38"])
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for chrom in CALL_CHROMS:
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if chrom in ("X", "Y") and sex == "U":
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continue
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if chrom == "Y" and sex == "F":
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continue
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sel = ctx["by_chrom"].get(chrom)
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if sel is None or len(sel) == 0:
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continue
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pos = pos_all[sel]
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in_par = np.zeros(len(sel), dtype=np.bool_)
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if chrom == "X":
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for a, b in par:
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in_par |= (pos >= a) & (pos <= b)
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regions = [(np.ones(len(sel), dtype=np.bool_), False)]
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if chrom == "X" and sex == "M":
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regions = [(in_par, False), (~in_par, True)]
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elif chrom == "Y":
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regions = [(np.ones(len(sel), dtype=np.bool_), True)]
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m_sp = median_spacing(pos)
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for rmask, haploid in regions:
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if rmask.sum() < 2:
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continue
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idx = sel[rmask]
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p, x_raw, b, gt = pos_all[idx], lrr[idx], baf[idx], geno[idx]
|
||||
x_seg = lrr_s[idx]
|
||||
states = hap if haploid else dip
|
||||
prior = np.array([s.prior for s in states])
|
||||
prior /= prior.sum()
|
||||
offset = float(np.nanmedian(x_raw)) if haploid else 0.0
|
||||
if not math.isfinite(offset):
|
||||
offset = 0.0
|
||||
prm = hmm.Params(seg_sd, baf_sd, lrr_offset=offset)
|
||||
e = hmm.emissions(states, x_seg, np.full(len(b), np.nan) if haploid else b, pfb[idx], prm)
|
||||
sw = hmm.switch_probs(p)
|
||||
path = hmm.viterbi(e, sw, prior)
|
||||
post = hmm.forward_backward(e, sw, prior)
|
||||
evs = extract(chrom, path, states, p)
|
||||
for ev in evs:
|
||||
annotate_stats(ev, p, x_raw, b, gt, post, states, m_sp, ctx["gamma"], haploid)
|
||||
evs = post_filter(evs, [x_raw[ev.i0 : ev.i1] for ev in evs], th, counts)
|
||||
for s_, e_ in _runs(path):
|
||||
st = states[int(path[s_])]
|
||||
segments.append({"chrom": chrom, "start": int(p[s_]), "end": int(p[e_ - 1]), "probes": e_ - s_,
|
||||
"state": st.name, "call": st.call, "cn": st.cn, "haploid": haploid,
|
||||
"posterior": float(post[s_:e_, int(path[s_])].mean())}) # fmt: skip
|
||||
base_cn = 1 if haploid else 2
|
||||
eff = effective_size(p, m_sp)
|
||||
if whole_chrom_only:
|
||||
evs = [ev for ev in evs if ev.effective_size >= 0.9 * eff]
|
||||
ploidy_num += base_cn * eff + sum((ev.cn - base_cn) * ev.effective_size for ev in evs)
|
||||
ploidy_den += eff
|
||||
events.extend((ev, haploid) for ev in evs)
|
||||
kept = apply_thresholds([ev for ev, _ in events], th, counts)
|
||||
kept = _mask_events(kept, ctx["mask"], counts)
|
||||
set_filters(kept, th, noisy)
|
||||
hap_of = {id(ev): h for ev, h in events}
|
||||
row = {
|
||||
"sample_id": si.sample_id, "sample_name": si.sample_name, "status": "OK", "logr_dev": logr_dev,
|
||||
"overall_ploidy": ploidy_num / max(ploidy_den, 1), "gc_correct": bool(gcfit and gcfit.applied),
|
||||
"gcwf": gcfit.gcwf if gcfit else math.nan, "sex_used": sex, "sex_source": sex_source,
|
||||
"n_del": sum(e.call == "DEL" for e in kept), "n_dup": sum(e.call == "DUP" for e in kept),
|
||||
"n_loh": sum(e.call == "LOH" for e in kept), "n_gainloh": sum(e.call == "GAINLOH" for e in kept),
|
||||
"n_mosaic": sum(e.mosaic for e in kept), "n_filtered": sum(counts.values()),
|
||||
"qc_flags": ";".join(flags),
|
||||
} # fmt: skip
|
||||
per_chr: dict[str, int] = {}
|
||||
for ev in kept:
|
||||
if ev.call in ("DEL", "DUP", "LOH"):
|
||||
per_chr[ev.chrom] = per_chr.get(ev.chrom, 0) + 1
|
||||
excess = [c for c, n in per_chr.items() if n > 10]
|
||||
if excess:
|
||||
row["qc_flags"] = ";".join([*flags, "excess_events:" + ",".join(excess)])
|
||||
row["lrr_sd_segmentation"] = seg_sd
|
||||
row["baf_sd"] = baf_sd
|
||||
return {"row": row, "events": kept, "haploid": hap_of, "segments": segments, "counts": counts}
|
||||
|
||||
|
||||
def _runs(path: npt.NDArray[np.int32]) -> list[tuple[int, int]]:
|
||||
if len(path) == 0:
|
||||
return []
|
||||
br = np.flatnonzero(np.diff(path) != 0) + 1
|
||||
return list(zip(np.r_[0, br].tolist(), np.r_[br, len(path)].tolist(), strict=True))
|
||||
|
||||
|
||||
def _mask_events(events: list[Any], mask: dict[str, list[tuple[int, int]]], counts: dict[str, int]) -> list[Any]:
|
||||
"""CYTO-017: trim to unmasked sequence; drop events ≥ 50 % masked."""
|
||||
out = []
|
||||
for ev in events:
|
||||
covered = 0
|
||||
for a, b in mask.get(ev.chrom, []):
|
||||
lo, hi = max(a, ev.start), min(b, ev.end)
|
||||
if lo <= hi:
|
||||
covered += hi - lo + 1
|
||||
if a <= ev.start <= b:
|
||||
ev.start = b + 1
|
||||
ev.flags.append("centromere_trimmed")
|
||||
if a <= ev.end <= b:
|
||||
ev.end = a - 1
|
||||
ev.flags.append("centromere_trimmed")
|
||||
if covered >= 0.5 * (ev.end - ev.start + 1 + covered) or ev.end < ev.start:
|
||||
counts["masked"] = counts.get("masked", 0) + 1
|
||||
continue
|
||||
out.append(ev)
|
||||
return out
|
||||
|
||||
|
||||
# ------------------------------------------------------------------------------------------------ VCF (CYTO-028..031)
|
||||
def _gt(ev: Any, haploid: bool, mode: str) -> str:
|
||||
if mode == "compat":
|
||||
return "1/1"
|
||||
if haploid:
|
||||
return "1"
|
||||
if ev.mosaic:
|
||||
return "0/1"
|
||||
if ev.call in ("LOH", "GAINLOH"):
|
||||
return "1/1"
|
||||
if ev.call == "DEL":
|
||||
return "1/1" if ev.cn == 0 else "0/1"
|
||||
return "./1" if ev.cn >= 4 else "0/1"
|
||||
|
||||
|
||||
def _fmt(v: float | None, nd: int) -> str:
|
||||
return "." if v is None or not math.isfinite(v) else f"{v:.{nd}f}"
|
||||
|
||||
|
||||
def vcf_text(
|
||||
sample_name: str,
|
||||
events: list[Any],
|
||||
haploid: dict[int, bool],
|
||||
contigs: list[tuple[str, int]],
|
||||
header: dict[str, str],
|
||||
opts: CnCallOptions,
|
||||
ref_base: Any,
|
||||
) -> tuple[str, list[tuple[str, int, int, str]]]:
|
||||
"""Header and records; also (chrom, beg0, end, line) for indexing."""
|
||||
th = opts.thresholds
|
||||
extra = {
|
||||
"smoothing": opts.smoothing,
|
||||
"max_mosaic_fraction": th.max_mosaic_fraction,
|
||||
"min_mosaic_fraction": f"{th.min_mosaic_fraction:.2f}",
|
||||
"filter_qual": th.filter_qual,
|
||||
"size_basis": "effective",
|
||||
"cn_cap": opts.cn_cap,
|
||||
"gt_mode": opts.gt_mode,
|
||||
"svlen_mode": opts.svlen_mode,
|
||||
}
|
||||
h = [
|
||||
"##fileformat=VCFv4.3",
|
||||
f"##source=SimurgArray {__version__} cn",
|
||||
f"##reference=file://{header['reference']}",
|
||||
f"##simurg_genome_build={header['build']}",
|
||||
f"##simurg_manifest={header['manifest']}",
|
||||
f"##simurg_cyto_model={header['model']}",
|
||||
"##simurg_thresholds=" + th.as_header(extra),
|
||||
f"##simurg_sex_used={header['sex']};source={header['sex_source']}",
|
||||
f"##OverallPloidy={float(header['ploidy']):.3f}",
|
||||
f"##GCCorrect={'true' if header['gc'] == 'True' else 'false'}",
|
||||
*(f"##contig=<ID={c},length={n}>" for c, n in contigs),
|
||||
'##ALT=<ID=DEL,Description="Copy number loss">',
|
||||
'##ALT=<ID=DUP,Description="Copy number gain">',
|
||||
'##ALT=<ID=LOH,Description="Absence/loss of heterozygosity (AOH/LOH/ROH)">',
|
||||
'##FILTER=<ID=PASS,Description="All filters passed">',
|
||||
f'##FILTER=<ID=Q{th.filter_qual},Description="Quality below {th.filter_qual}">',
|
||||
'##FILTER=<ID=SampleQuality,Description="Sample flagged as potentially low quality: LRR SD above 0.2">',
|
||||
f'##FILTER=<ID=LowFraction,Description="Mosaic event with estimated mosaic fraction below '
|
||||
f'{th.min_mosaic_fraction:.2f}">',
|
||||
'##INFO=<ID=END,Number=1,Type=Integer,Description="Last base of the event (1-based, inclusive)">',
|
||||
'##INFO=<ID=SVTYPE,Number=1,Type=String,Description="DEL, DUP or LOH">',
|
||||
'##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Event length in bp; negative for deletions">',
|
||||
'##INFO=<ID=EFFLEN,Number=1,Type=Integer,Description="Effective length in bp (gaps above 150x median probe '
|
||||
'spacing replaced by the median spacing)">',
|
||||
'##INFO=<ID=PROBE,Number=1,Type=Integer,Description="Number of probes in the event">',
|
||||
'##INFO=<ID=MOSAIC,Number=0,Type=Flag,Description="Mosaic event">',
|
||||
'##INFO=<ID=HIGHFRACTION,Number=0,Type=Flag,Description="Mosaic event promoted to constitutional because its '
|
||||
'mosaic fraction reached the maximum">',
|
||||
'##INFO=<ID=LOHTYPE,Number=1,Type=String,Description="AOH (constitutional, copy-neutral or gain), CNLOH '
|
||||
'(mosaic copy-neutral), GAINLOH (mosaic copy-gain)">',
|
||||
'##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype (see SimurgArray docs, CYTO-031)">',
|
||||
f'##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number; the maximum value {opts.cn_cap} means '
|
||||
f'{opts.cn_cap} or more">',
|
||||
'##FORMAT=<ID=NR,Number=1,Type=Float,Description="Aggregated normalized intensity (median 2^LRR; about CN/2)">',
|
||||
'##FORMAT=<ID=LRD,Number=1,Type=Float,Description="Standard deviation of LRR within the event">',
|
||||
'##FORMAT=<ID=MF,Number=1,Type=Float,Description="Estimated mosaic fraction; missing if not mosaic or not '
|
||||
'estimable">',
|
||||
f"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t{sample_name}",
|
||||
]
|
||||
order = {c: i for i, (c, _) in enumerate(contigs)}
|
||||
recs = []
|
||||
for ev in sorted(events, key=lambda e: (order.get(e.chrom, 999), e.start, e.end)):
|
||||
s_, e_ = ev.start, ev.end
|
||||
pos = s_ - 1 if s_ > 1 else 1
|
||||
ref = ref_base(ev.chrom, pos)
|
||||
length = e_ - s_ + 1
|
||||
svlen = -length if ev.svtype == "DEL" and opts.svlen_mode == "signed" else length
|
||||
info = [f"END={e_}", f"SVTYPE={ev.svtype}", f"SVLEN={svlen}", f"EFFLEN={ev.effective_size}",
|
||||
f"PROBE={ev.probes}"] # fmt: skip
|
||||
if ev.mosaic:
|
||||
info.append("MOSAIC")
|
||||
if ev.high_fraction:
|
||||
info.append("HIGHFRACTION")
|
||||
lt = {"LOH": "AOH", "GAINLOH": "AOH", "MLOH": "CNLOH"}.get(ev.call)
|
||||
if ev.call == "GAINLOH" and ev.mosaic:
|
||||
lt = "GAINLOH"
|
||||
if lt:
|
||||
info.append(f"LOHTYPE={lt}")
|
||||
cn = min(ev.cn, opts.cn_cap)
|
||||
mf = ev.mosaic_fraction if ev.mosaic or ev.high_fraction else None
|
||||
line = (f"{ev.chrom}\t{pos}\t{ev.id_prefix}:{ev.chrom}:{s_}-{e_}\t{ref}\t<{ev.svtype}>\t{int(ev.quality)}\t"
|
||||
f"{';'.join(ev.filters)}\t{';'.join(info)}\tGT:CN:NR:LRD:MF\t"
|
||||
f"{_gt(ev, haploid.get(id(ev), False), opts.gt_mode)}:{cn}:{_fmt(ev.nr, 4)}:{_fmt(ev.lrd, 4)}:"
|
||||
f"{_fmt(mf, 3)}") # fmt: skip
|
||||
recs.append((ev.chrom, pos - 1, e_, line))
|
||||
return "\n".join(h) + "\n", recs
|
||||
|
||||
|
||||
def write_vcf(path: Path, header: str, recs: list[tuple[str, int, int, str]], bgzip: bool) -> None:
|
||||
from simurg.core.atomic import atomic_open
|
||||
from simurg.formats.bgzf import BgzfWriter, TabixBuilder, write_tbi
|
||||
|
||||
tbx = TabixBuilder()
|
||||
with atomic_open(path, "wb") as raw:
|
||||
if bgzip:
|
||||
w = BgzfWriter(raw) # type: ignore[arg-type]
|
||||
w.write_record(header.encode())
|
||||
for chrom, beg, end, line in recs:
|
||||
vs, ve = w.write_record((line + "\n").encode())
|
||||
tbx.add(chrom, beg, end, vs, ve)
|
||||
w.close()
|
||||
else:
|
||||
raw.write((header + "".join(r[3] + "\n" for r in recs)).encode()) # type: ignore[arg-type]
|
||||
if bgzip:
|
||||
write_tbi(Path(str(path) + ".tbi"), tbx)
|
||||
|
||||
|
||||
# ------------------------------------------------------------------------------------------------ batch driver
|
||||
_W: dict[str, Any] = {}
|
||||
|
||||
|
||||
def _init_worker(path: str) -> None:
|
||||
import pickle
|
||||
|
||||
with open(path, "rb") as fh:
|
||||
_setup(pickle.load(fh))
|
||||
|
||||
|
||||
def _setup(state: dict[str, Any]) -> None:
|
||||
_W.update(state)
|
||||
fasta = state["opts"].fasta
|
||||
if fasta is not None:
|
||||
genome = Genome(fasta)
|
||||
_W["genome"] = genome
|
||||
_W["cmap"] = ContigMap([e.name for e in genome.entries], "auto")
|
||||
|
||||
|
||||
def _work(si: SampleInput) -> dict[str, Any]:
|
||||
ctx, opts = _W["ctx"], _W["opts"]
|
||||
try:
|
||||
res = call_sample(si, ctx, opts)
|
||||
except Exception as e: # CYTO-040: one sample never stops the batch
|
||||
code = e.code if isinstance(e, SimurgError) else "E_CN_FAILED"
|
||||
return {"row": {"sample_id": si.sample_id, "sample_name": si.sample_name, "status": "FAILED",
|
||||
"qc_flags": f"{code}: {e}"}, "events": [], "error": code} # fmt: skip
|
||||
row = res["row"]
|
||||
genome = _W.get("genome")
|
||||
|
||||
def ref_base(chrom: str, pos: int) -> str:
|
||||
if genome is None:
|
||||
return "N"
|
||||
contig = _W["cmap"].get(chrom)
|
||||
return genome.fetch(contig, pos - 1, pos) or "N" if contig else "N"
|
||||
|
||||
header = {**_W["vcf_header"], "sex": row["sex_used"], "sex_source": row["sex_source"],
|
||||
"ploidy": str(row["overall_ploidy"]), "gc": str(row["gc_correct"])} # fmt: skip
|
||||
htxt, recs = vcf_text(si.sample_name, res["events"], res["haploid"], ctx["contigs"], header, opts, ref_base)
|
||||
out = opts.out / f"{si.sample_id}.cyto.cnv.vcf{'.gz' if opts.bgzip else ''}"
|
||||
write_vcf(out, htxt, recs, opts.bgzip)
|
||||
seg = pa.Table.from_pylist(res["segments"]) if res["segments"] else pa.table({"chrom": pa.array([], pa.string())})
|
||||
pq.write_table(seg, opts.out / f"{si.sample_id}.cn_segments.parquet", compression="zstd")
|
||||
evs = [
|
||||
{"id": f"{ev.id_prefix}:{ev.chrom}:{ev.start}-{ev.end}", "chrom": ev.chrom, "start": ev.start, "end": ev.end,
|
||||
"call_type": ev.svtype, "call": ev.call, "loh_type": ev.loh_type, "mosaic": ev.mosaic,
|
||||
"mosaic_fraction": ev.mosaic_fraction, "high_fraction": ev.high_fraction, "copy_number": ev.cn,
|
||||
"quality": round(ev.quality, 1), "filters": ev.filters, "size": ev.size, "effective_size": ev.effective_size,
|
||||
"probe_count": ev.probes, "percent_het": ev.percent_het, "lrr_median": ev.lrr_median, "lrr_dev": ev.lrd,
|
||||
"baf_dev": ev.baf_dev, "nr": ev.nr, "flags": ev.flags}
|
||||
for ev in res["events"]
|
||||
] # fmt: skip
|
||||
return {"row": row, "events": evs, "counts": res["counts"]}
|
||||
|
||||
|
||||
def _read_summary(path: Path | None) -> dict[str, dict[str, str]]:
|
||||
if path is None or not path.exists():
|
||||
return {}
|
||||
lines = path.read_text(encoding="utf-8").splitlines()
|
||||
head = lines[0].split("\t")
|
||||
return {r[0]: dict(zip(head, r, strict=False)) for r in (ln.split("\t") for ln in lines[1:] if ln)}
|
||||
|
||||
|
||||
def run_cn_call(opts: CnCallOptions, rep: Reporter) -> int:
|
||||
"""``simurg cn call`` (CLI-028)."""
|
||||
import multiprocessing as mp
|
||||
import os
|
||||
import pickle
|
||||
import tempfile
|
||||
from concurrent.futures import ProcessPoolExecutor
|
||||
|
||||
from simurg.core.atomic import atomic_write_text, check_outputs_absent
|
||||
from simurg.core.provenance import RunManifest
|
||||
from simurg.formats.discovery import discover_gtcs
|
||||
from simurg.pipeline.qc import write_tsv
|
||||
|
||||
rm = RunManifest(command="cn call", argv=opts.argv)
|
||||
rep.run_id = rm.run_id
|
||||
if opts.gtcs is None:
|
||||
raise SimurgError("E_NO_INPUT", "give --gtcs (folder of GTC files)")
|
||||
gtcs = discover_gtcs(opts.gtcs)
|
||||
summary_path = opts.summary or (opts.gtcs / "sample_summary.tsv")
|
||||
summary = _read_summary(summary_path)
|
||||
ext = ".cyto.cnv.vcf.gz" if opts.bgzip else ".cyto.cnv.vcf"
|
||||
check_outputs_absent(
|
||||
[opts.out / f"{k}{ext}" for k in gtcs] + [opts.out / "cn_sample_summary.tsv"], force=opts.force
|
||||
)
|
||||
th = opts.thresholds
|
||||
for k in list(th.probes):
|
||||
if th.probes[k] < 10:
|
||||
rep.warn("W_CN_PROBE_FLOOR", f"--min-{k}-probes {th.probes[k]} raised to 10")
|
||||
th.probes[k] = 10
|
||||
man = read_bpm(opts.bpm)
|
||||
model = read_model(opts.model, man)
|
||||
build = str(model.header.get("genome_build") or "GRCh38")
|
||||
chroms = np.array(["X" if c == "XY" else (c[3:] if c.lower().startswith("chr") else c) for c in man.chroms])
|
||||
pos = man.map_infos.astype(np.int64)
|
||||
by_chrom = {}
|
||||
for c in CALL_CHROMS:
|
||||
sel = np.flatnonzero((chroms == c) & (pos > 0))
|
||||
by_chrom[c] = sel[np.argsort(pos[sel], kind="stable")]
|
||||
auto = np.isin(chroms, CALL_CHROMS[:22]) & (pos > 0)
|
||||
genome = None
|
||||
cmap = None
|
||||
lengths: dict[str, int] = {}
|
||||
if opts.fasta is not None:
|
||||
genome = Genome(opts.fasta)
|
||||
cmap = ContigMap([e.name for e in genome.entries], "auto")
|
||||
for c in CALL_CHROMS:
|
||||
contig = cmap.get(c)
|
||||
if contig:
|
||||
lengths[c] = genome.contig_length(contig)
|
||||
else:
|
||||
rep.warn("W_CN_NO_FASTA", "no --fasta: VCF REF padding bases are written as N")
|
||||
contigs = [(c, lengths.get(c, int(pos[by_chrom[c]].max()) if len(by_chrom[c]) else 0)) for c in CALL_CHROMS
|
||||
if len(by_chrom[c])] # fmt: skip
|
||||
ctx = {"chroms": chroms, "pos": pos, "model": model, "auto": auto, "by_chrom": by_chrom, "build": build,
|
||||
"mask": read_mask(opts.mask_bed, build), "gamma": 0.5, "contigs": contigs} # fmt: skip
|
||||
model_sha = hashlib.sha256(opts.model.read_bytes()).hexdigest()
|
||||
man_sha = hashlib.sha256(opts.bpm.read_bytes()).hexdigest()
|
||||
schema = model.header.get("schema_version")
|
||||
vcf_header = {
|
||||
"reference": str(opts.fasta.resolve()) if opts.fasta else "none",
|
||||
"build": build,
|
||||
"manifest": f"{man.manifest_name};sha256={man_sha}",
|
||||
"model": f"{opts.model.name};sha256={model_sha};schema={schema}",
|
||||
}
|
||||
samples = []
|
||||
for k, path in gtcs.items():
|
||||
r = summary.get(k, {})
|
||||
sex = r.get("sex_est", "U") or "U"
|
||||
src = "summary" if sex in ("M", "F") else "none"
|
||||
if sex not in ("M", "F") and r.get("sex_reported") in ("M", "F"):
|
||||
sex, src = r["sex_reported"], "sheet"
|
||||
try:
|
||||
ld = float(r.get("logr_dev", "nan"))
|
||||
except ValueError:
|
||||
ld = math.nan
|
||||
samples.append(SampleInput(k, r.get("sample_name", k) or k, str(path), sex, ld, src))
|
||||
opts.out.mkdir(parents=True, exist_ok=True)
|
||||
state = {"ctx": ctx, "opts": opts, "vcf_header": vcf_header}
|
||||
workers = max(1, min(opts.threads or (os.cpu_count() or 1), len(samples)))
|
||||
rep.info(f"CN calling of {len(samples)} sample(s) with {workers} worker(s)")
|
||||
if workers == 1:
|
||||
_setup(state)
|
||||
try:
|
||||
results = [_work(s) for s in samples]
|
||||
finally:
|
||||
_W.clear()
|
||||
else:
|
||||
fd, sp = tempfile.mkstemp(prefix=".simurg-workers-", suffix=".pkl", dir=opts.out)
|
||||
try:
|
||||
with os.fdopen(fd, "wb") as fh:
|
||||
pickle.dump(state, fh, protocol=5)
|
||||
with ProcessPoolExecutor(workers, mp_context=mp.get_context("spawn"), initializer=_init_worker,
|
||||
initargs=(sp,)) as ex: # fmt: skip
|
||||
results = list(ex.map(_work, samples))
|
||||
finally:
|
||||
Path(sp).unlink(missing_ok=True)
|
||||
cols = ["sample_id", "sample_name", "status", "logr_dev", "overall_ploidy", "gc_correct", "gcwf", "sex_used",
|
||||
"sex_source", "n_del", "n_dup", "n_loh", "n_gainloh", "n_mosaic", "n_filtered", "qc_flags"] # fmt: skip
|
||||
rows = []
|
||||
for s, res in zip(samples, results, strict=True):
|
||||
row = {**res["row"], "sample_folder": str(Path(s.gtc).parent)}
|
||||
if row["status"] != "OK":
|
||||
rep.error(res.get("error", "E_CN_FAILED"), f"{s.sample_id}: {row['qc_flags']}", sample_id=s.sample_id)
|
||||
elif row["sex_source"] == "resolved":
|
||||
rep.info(f"Sample {s.sample_id} sex updated from U to {row['sex_used']}", "I_CN_SEX_RESOLVED")
|
||||
rows.append(row)
|
||||
write_tsv(opts.out / "cn_sample_summary.tsv", cols, rows)
|
||||
th_dict = {f"min_{k}_probes": th.probes[k] for k in th.probes} | {
|
||||
f"min_{k}_size_bp": th.size_bp[k] for k in th.size_bp
|
||||
}
|
||||
sidecar = {
|
||||
"schema": "simurg.cn_call/1", "software": f"SimurgArray {__version__}", "run_id": rm.run_id,
|
||||
"genome_build": build, "model": vcf_header["model"], "manifest": vcf_header["manifest"],
|
||||
"summary": str(summary_path) if summary else None,
|
||||
"thresholds": th_dict | {"max_mosaic_fraction": th.max_mosaic_fraction,
|
||||
"min_mosaic_fraction": th.min_mosaic_fraction, "filter_qual": th.filter_qual,
|
||||
"smoothing": opts.smoothing, "cn_cap": opts.cn_cap, "size_basis": "effective"},
|
||||
"samples": [{**r["row"], "events": r["events"]} for r in results],
|
||||
} # fmt: skip
|
||||
atomic_write_text(opts.out / "cn_call_manifest.json", json.dumps(sidecar, indent=1, default=_json_default))
|
||||
ok = sum(r["row"]["status"] == "OK" for r in results)
|
||||
rm.summary = {"samples": len(results), "ok": ok}
|
||||
rm.status = "completed"
|
||||
rm.write(opts.out / "run_manifest.json")
|
||||
rep.info(f"done: {ok}/{len(results)} samples; {sum(len(r['events']) for r in results)} events")
|
||||
if ok == len(results):
|
||||
return ExitCode.OK
|
||||
return ExitCode.PARTIAL if ok else ExitCode.ALL_FAILED
|
||||
|
||||
|
||||
def _json_default(v: Any) -> Any:
|
||||
if isinstance(v, np.generic):
|
||||
return v.item()
|
||||
if isinstance(v, float) and not math.isfinite(v):
|
||||
return None
|
||||
raise TypeError(type(v))
|
||||
Reference in new issue
Block a user