kemal
17bd0e8f78
- tests/oracle/test_p2_raw_xy.py: IDAT-assembled raw X/Y and controls equal the arrays in oracle GTCs - validate_p1_large.py: phase-P2 comparison against vendor GTCs with diagnostics (channel swap, bead-count disagreements) - cloud trial: also runs `simurg ingest` on all samples (time/memory), disk 250 GB
37 lines
1.3 KiB
Python
37 lines
1.3 KiB
Python
"""Phase P2 acceptance on P0 data: raw X/Y and control intensities assembled from IDATs equal the arrays stored
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in oracle GTCs (TOC 1000/1001, 500/501). The same check on vendor GTCs runs in scripts/validate_p1_large.py --p2.
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"""
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from __future__ import annotations
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import numpy as np
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import pytest
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from simurg.formats.bpm import read_bpm
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from simurg.formats.gtc import read_gtc
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from simurg.formats.idat import read_idat
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from simurg.signal.raw_xy import LocusMapCache, assemble_raw_xy, check_coverage
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from tests.conftest import GSA_BPM, GSA_IDATS, ORACLE_GTCS, need
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pytestmark = pytest.mark.data
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def test_raw_xy_equals_oracle_gtcs() -> None:
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need(GSA_BPM, GSA_IDATS, ORACLE_GTCS)
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m = read_bpm(GSA_BPM)
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cache = LocusMapCache(m)
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gtcs = sorted(ORACLE_GTCS.glob("*.gtc"))
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assert gtcs
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for g in gtcs:
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sid = g.stem
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chip = sid.split("_")[0]
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grn = read_idat(GSA_IDATS / chip / f"{sid}_Grn.idat")
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red = read_idat(GSA_IDATS / chip / f"{sid}_Red.idat")
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assert check_coverage(grn, m)[0] == 1.0
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raw = assemble_raw_xy(grn, red, m, cache=cache)
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ref = read_gtc(g)
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assert np.array_equal(raw.raw_x, ref.raw_x), sid
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assert np.array_equal(raw.raw_y, ref.raw_y), sid
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assert np.array_equal(raw.controls_x, ref.controls_x), sid
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assert np.array_equal(raw.controls_y, ref.controls_y), sid
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