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Tags:
population-genetics
demographic-inference
effective-population-size
coalescent
msprime
simulation
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File size: 5,001 Bytes
ee5b44c | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 | 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
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