feat(ptm): stratified AF-depletion analysis (hvantk ptm constraint)#89
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feat(ptm): stratified AF-depletion analysis (hvantk ptm constraint)#89
hvantk ptm constraint)#89Conversation
The file was rewritten for AnnData during scverse migration but kept the Hail-era filename. The leftover Hail histogram function had no live callers (only @pytest.mark.hail tests against removed Hail builders) and a broken ``"ad.AnnData"`` annotation that triggered an F821 lint error. - New hvantk/visualization/expression/anndata.py exposes visualize_expression_distribution(adata, ...) operating on adata.X. - Old hail.py removed; visualization facade and subpackage doc updated. - Test import switched to the new module.
…ze_expression_ad Completes the cleanup planned in the scverse-integration plan (Task 10 step 5). The Hail-based functions in matrix_utils.py were superseded by their _ad equivalents when expression I/O migrated to AnnData; their only remaining callers were two skipped @pytest.mark.hail test files. - Remove annotate_column_summary, describe_expression_mt, summarize_expression, summarize_matrix, filter_by_metadata, filter_by_gene_list, filter_by_expression, get_top_expressed_genes (and the optional hail import). - Delete tests/test_matrix_utils.py and tests/test_summarize_expression.py. - summarize_expression_ad: stop mutating adata.obs (was writing _group_label into the caller's object) and replace the per-row index.get_loc lookup with groupby indices for O(n_cells) splitting. - gene_sets.py: refresh extract_marker_gene_sets docstring to point at the AnnData summarizer and note its long-format output requires pivot or scanpy rank_genes_groups for direct use.
…hail_context - converters.anndata_to_hail_mt previously built the long-format DataFrame with a Python double loop over n_obs * n_var entries (200M dict allocs for a modest 10k x 20k matrix). Replace with np.repeat / np.tile / X.ravel — single pass, no Python loop. - The np.bool monkey-patch (Hail 0.2.x compat with NumPy >= 1.24) lived as a side-effect at the top of converters.py. Move it into hail_context.py so it runs before any Hail import regardless of which module pulls Hail in first. converters.py now imports hl via hail_context to guarantee the shim is applied.
test_dataset_download_returns_intermediate_tsv mocked urllib.request.urlretrieve, but the production code calls requests.get. The mock was a no-op, so the test attempted a real network download and hung pytest -q indefinitely. Mock requests.get with a context-manager fake response that streams the bundled fixture zip.
- matrix_builders.py, cptac.py, expression_atlas.py: remove inner ``import anndata as ad`` repeats inside builder functions; module-level import already in scope. - test_matrix_utils_anndata.py: replace the importlib.util workaround (which sidestepped hvantk.utils.__init__ over a non-existent Python 3.10 syntax issue) with a plain import. Project requires Python >= 3.10 where PEP 604 unions are valid.
Implements the `hvantk ptm constraint` CLI and `hvantk.ptm.constraint` module from the 2026-04-13 implementation plan. Compares gnomAD allele- frequency distributions between PTM-proximal and non-PTM variants, stratified by tissue, cell type, or any categorical metadata field. Modules added: - hvantk/ptm/constraint.py — orchestrator, PTMConstraintConfig/Result, five statistical tests (per-group ranking, τ quartile, τ × LOEUF factorial, PTM category × group heatmap, within-gene Wilcoxon) - hvantk/ptm/constraint_expression.py — unified backend adapter for Hail MatrixTable / AnnData / tabular expression sources - hvantk/ptm/constraint_plots.py — four-panel figure renderer - hvantk/ptm/constraint_report.py — self-contained HTML report - hvantk/utils/tissue_specificity.py — thin tspex wrapper for τ / TSI / Gini / Shannon metrics Wiring: - hvantk/commands/ptm_cli.py — `ptm constraint` subcommand - hvantk/ptm/__init__.py — lazy exports for the new API - pyproject.toml — `constraint` extra (tspex, matplotlib, seaborn) Docs: - docs_site/tools/ptm-constraint.md - docs_site/guide/usage.md (10-line recipe) - docs_site/architecture.md (module index) Tests: 6 smoke tests in hvantk/tests/test_ptm_constraint.py. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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Not up to standards ⛔🔴 Issues
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| Category | Results |
|---|---|
| UnusedCode | 2 medium |
| Documentation | 30 minor |
| ErrorProne | 5 high |
| Security | 3 medium 19 high |
| CodeStyle | 1 minor |
| Complexity | 14 medium |
🟢 Metrics 186 complexity · 5 duplication
Metric Results Complexity 186 Duplication 5
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…ield Code-review follow-ups to the initial constraint implementation: - _anndata_value_column unconditionally returned "mean", so --expression-metric median and median_nonzero were silent no-ops on the AnnData backend. Replaced the value-column helper with a direct numpy aggregation (_aggregate_anndata_direct) that runs per-group np.median / np.nanmedian (for nonzero) over adata.X when the user requests a median metric. - _load_variants silently skipped label filtering when the configured label_field was absent from the variants HT, leading to results that claim to be filtered to TN/TP but actually include every label. Now raises ValueError with a clear remediation hint unless the user explicitly passes --label-filter all. - pyproject.toml + requirements.txt: added tspex so CI (which installs from requirements.txt) can import the wrapper and the constraint smoke tests do not fail with ImportError. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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Code reviewNo issues found. Checked for bugs and CLAUDE.md compliance against the constraint feature files ( 🤖 Generated with Claude Code - If this code review was useful, please react with 👍. Otherwise, react with 👎. |
The Conda CI workflow has been failing since the AnnData migration landed on dev because environment.yml never gained anndata/scanpy. The constraint work also needs tspex; add it alongside so `python-package- conda.yml` can import every test module. Added: anndata, scanpy, pysam, PyYAML, psutil, scikit-learn, tspex.
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Summary
hvantk ptm constraint— a stratified allele-frequency depletion analysis that compares gnomAD AF distributions between PTM-proximal and non-PTM variants, grouped by tissue / cell-type / custom metadata fields. Turns the multi-dataset EDA prototyped in Notebooks E–I (GTEx RNA, GTEx protein, HCA adult, Farah mid-fetal, Asp early fetal) into a reusable CLI.hvantk/ptm/:constraint.py(orchestrator + 5 statistical tests),constraint_expression.py(Hail MT / AnnData / tabular backend adapter),constraint_plots.py(4-panel figure renderer),constraint_report.py(self-contained HTML report). τ computation is delegated to the maintainedtspexpackage via a thin wrapper inhvantk/utils/tissue_specificity.py.Test plan
pytest hvantk/tests/test_ptm_constraint.py— 6 smoke tests pass (tspex-vs-Yanai reference, tabular / AnnData adapter contracts, config validation, gene-feature computation, CLI help).hvantk ptm --helpandhvantk ptm constraint --helprender cleanly.Refs:
local/planning/2026-04-13-hvantk-ptm-constraint-implementation-plan.md,local/planning/2026-04-13-ptm-constraint-design.md.🤖 Generated with Claude Code