Datasets:
Formats:
parquet
Size:
100K - 1M
Tags:
population-genetics
demographic-inference
effective-population-size
coalescent
msprime
simulation
License:
| from __future__ import annotations | |
| import numpy as np | |
| import pytest | |
| import simulator.empirical_maps as empirical_maps_module | |
| from simulator.config import Config | |
| from simulator.empirical_maps import ( | |
| EmpiricalMapStore, | |
| PiecewiseRateMap, | |
| load_empirical_rate_table, | |
| slice_piecewise_map, | |
| ) | |
| from simulator.maps import sample_maps_for_source | |
| def _rate_map(chrom: str, positions: list[float], rates: list[float]) -> PiecewiseRateMap: | |
| return PiecewiseRateMap( | |
| chrom=chrom, | |
| position=np.asarray(positions, dtype=np.float64), | |
| rate=np.asarray(rates, dtype=np.float64), | |
| ) | |
| def test_common_chroms_require_a_shared_coordinate_span() -> None: | |
| store = EmpiricalMapStore( | |
| rec_maps={"chr1": _rate_map("chr1", [100, 250, 400], [1e-8, 2e-8])}, | |
| mut_maps={"chr1": _rate_map("chr1", [120, 300, 500], [3e-8, 4e-8])}, | |
| ) | |
| assert store.common_slice_start_bounds("chr1", 280) == (120.0, 120.0) | |
| assert store.common_chroms(280) == ["chr1"] | |
| assert store.common_chroms(281) == [] | |
| def test_slice_piecewise_map_accepts_an_explicit_start_and_exact_end_boundary() -> None: | |
| rate_map = _rate_map("chr1", [100, 150, 250, 400], [1e-8, 2e-8, 3e-8]) | |
| pos, true_rate, obs_pos, _, meta = slice_piecewise_map( | |
| np.random.default_rng(1), | |
| rate_map, | |
| length=100, | |
| obs_noise_sigma=0.0, | |
| baseline_rate=1e-8, | |
| start=150, | |
| ) | |
| np.testing.assert_array_equal(pos, [0.0, 100.0]) | |
| np.testing.assert_array_equal(obs_pos, pos) | |
| np.testing.assert_array_equal(true_rate, [2e-8]) | |
| assert meta["slice_start_bp"] == 150.0 | |
| assert meta["slice_end_bp"] == 250.0 | |
| def test_empirical_source_uses_one_colocated_interval_for_both_maps() -> None: | |
| cfg = Config(seq_len=100, baseline_rec=1e-8, baseline_mu=1e-8, observed_map_noise=0.0) | |
| store = EmpiricalMapStore( | |
| rec_maps={"chr1": _rate_map("chr1", [100, 200, 300, 400], [1e-8, 2e-8, 3e-8])}, | |
| mut_maps={"chr1": _rate_map("chr1", [120, 220, 320, 420], [4e-8, 5e-8, 6e-8])}, | |
| ) | |
| *_, meta = sample_maps_for_source( | |
| np.random.default_rng(7), | |
| cfg, | |
| "empirical_map_slice", | |
| store, | |
| ) | |
| rec_meta = meta["rec_slice"] | |
| mut_meta = meta["mut_slice"] | |
| assert meta["slice_alignment"] == "shared_chromosomal_interval" | |
| assert meta["slice_chrom"] == rec_meta["chrom"] == mut_meta["chrom"] == "chr1" | |
| assert meta["slice_start_bp"] == rec_meta["slice_start_bp"] == mut_meta["slice_start_bp"] | |
| assert meta["slice_end_bp"] == rec_meta["slice_end_bp"] == mut_meta["slice_end_bp"] | |
| assert meta["slice_end_bp"] - meta["slice_start_bp"] == pytest.approx(cfg.seq_len) | |
| assert 120.0 <= meta["slice_start_bp"] <= 300.0 | |
| def test_explicit_start_must_fit_inside_the_source_map() -> None: | |
| rate_map = _rate_map("chr1", [100, 200, 300], [1e-8, 2e-8]) | |
| with pytest.raises(ValueError, match="outside the valid range"): | |
| slice_piecewise_map( | |
| np.random.default_rng(1), | |
| rate_map, | |
| length=100, | |
| obs_noise_sigma=0.0, | |
| baseline_rate=1e-8, | |
| start=201, | |
| ) | |
| def test_non_finite_empirical_coordinates_are_rejected(tmp_path) -> None: | |
| path = tmp_path / "invalid-map.bed" | |
| path.write_text( | |
| "chr1 0 100 1e-8\n" | |
| "chr1 100 inf 2e-8\n", | |
| encoding="utf-8", | |
| ) | |
| with pytest.raises(ValueError, match="non-finite"): | |
| load_empirical_rate_table( | |
| str(path), | |
| baseline_rate=1e-8, | |
| map_kind="recombination", | |
| ) | |
| def test_non_finite_manual_rate_map_is_rejected_before_slicing() -> None: | |
| rate_map = _rate_map("chr1", [0.0, 100.0], [float("inf")]) | |
| with pytest.raises(ValueError, match="non-finite"): | |
| slice_piecewise_map( | |
| np.random.default_rng(1), | |
| rate_map, | |
| length=50, | |
| obs_noise_sigma=0.0, | |
| baseline_rate=1e-8, | |
| ) | |
| def test_common_span_validation_is_cached_off_the_sample_hot_path( | |
| monkeypatch: pytest.MonkeyPatch, | |
| ) -> None: | |
| store = EmpiricalMapStore( | |
| rec_maps={"chr1": _rate_map("chr1", [0, 100, 200], [1e-8, 2e-8])}, | |
| mut_maps={"chr1": _rate_map("chr1", [0, 120, 220], [3e-8, 4e-8])}, | |
| ) | |
| original = empirical_maps_module._validate_piecewise_rate_map | |
| calls = 0 | |
| def counted(rate_map: PiecewiseRateMap) -> None: | |
| nonlocal calls | |
| calls += 1 | |
| original(rate_map) | |
| monkeypatch.setattr(empirical_maps_module, "_validate_piecewise_rate_map", counted) | |
| assert store.is_available(100) | |
| assert store.is_available(100) | |
| assert store.common_chroms(100) == ["chr1"] | |
| assert store.common_slice_start_bounds("chr1", 100) == (0.0, 100.0) | |
| assert calls == 2 | |
| cfg = Config(seq_len=100, observed_map_noise=0.0) | |
| sample_maps_for_source(np.random.default_rng(3), cfg, "empirical_map_slice", store) | |
| sample_maps_for_source(np.random.default_rng(4), cfg, "empirical_map_slice", store) | |
| assert calls == 2 | |