File size: 2,078 Bytes
9d901ad | 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 | """Integration test: full pipeline on synthetic data."""
import numpy as np
import pytest
def test_full_pipeline(synthetic_adata):
"""Run the complete scPTR pipeline on synthetic data."""
import scptr
adata = synthetic_adata
# Preprocessing
scptr.pp.filter_genes(adata, min_unspliced_counts=1, min_unspliced_cells=1)
scptr.pp.normalize_layers(adata)
scptr.pp.neighbors(adata, n_neighbors=30)
scptr.pp.smooth_layers(adata)
assert "Mu" in adata.layers
assert "Ms" in adata.layers
# Core estimation
scptr.tl.estimate_beta(adata)
scptr.tl.estimate_gamma(adata)
scptr.tl.variance_decomposition(adata)
assert "beta" in adata.var.columns
assert "gamma" in adata.layers
assert "tf_score" in adata.var.columns
assert "ptf_score" in adata.var.columns
# PT states
scptr.tl.pt_states(adata)
assert "pt_state" in adata.obs.columns
assert "X_gamma_pca" in adata.obsm
assert "X_gamma_umap" in adata.obsm
# Rank genes
result = scptr.tl.rank_pt_genes(adata)
assert len(result) > 0
# PT velocity
scptr.tl.pt_velocity(adata)
assert "pt_velocity" in adata.layers
assert adata.layers["pt_velocity"].shape == adata.shape
# Check all uns parameters logged
assert "scptr" in adata.uns
params = adata.uns["scptr"]
for step in [
"filter_genes", "normalize_layers", "neighbors",
"smooth_layers", "estimate_beta", "estimate_gamma",
"variance_decomposition", "pt_states", "rank_pt_genes",
"pt_velocity",
]:
assert step in params, f"Missing params for {step}"
def test_network_inference(analyzed_adata):
"""Test network inference on analyzed data."""
import scptr
# Use a small subset of genes as regulators/targets for speed
genes = analyzed_adata.var_names[:20].tolist()
result = scptr.tl.infer_network(
analyzed_adata,
regulators=genes,
targets=genes[:5],
)
assert "pt_network" in analyzed_adata.uns
assert "infer_network" in analyzed_adata.uns["scptr"]
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