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Development Notes

Local Environment

Use a local virtual environment:

python3 -m venv .venv
source .venv/bin/activate
python -m pip install --upgrade pip
pip install -e .[dev]

This project packages the Python-side workflow logic, but still expects the external RNA analysis toolchain to be installed separately and available on PATH.

Workflow Entry Points

There are two workflow entry points in the repository:

The packaged CLI rnaconsnake-run invokes workflow files copied from those root files at build time. In editable development installs, the CLI falls back to the root workflow files directly.

For repository-local use without shell-activating a virtual environment, the root launcher rnaconsnake-run executes python -m rnaconsnake.cli with PYTHONPATH=src and automatically prefers ./.venv/bin/python when it exists.

Important preprocessing knobs in config.yaml:

  • remove_gaponly_gapratio Maximum allowed gap fraction per sequence.
  • remove_gaponly_max_n Maximum allowed count of N/n characters per sequence. The default is 0, which removes any sequence containing ambiguous N bases.
  • do_rscape Enable optional per-hit R-scape analysis and summary integration.

Common Commands

pytest -v
rnaconsnake-run --input-alignment /path/to/input.stk --output-dir /path/to/run_dir
rnaconsnake-run --check-deps
rnaconsnake-run --version

Example CLI override for window sizes:

rnaconsnake-run --input-alignment /path/to/input.stk --maxbpspan 150 --maxbpspan 250 --cores all

Optional R-scape branch:

rnaconsnake-run --input-alignment /path/to/input.stk --rscape --cores all
rnaconsnake-run --check-deps --rscape

RNAz defaults to -d -n, so alignment shuffling is disabled unless explicitly requested. To allow shuffling for a run:

rnaconsnake-run --input-alignment /path/to/input.stk --rnaz-shuffle --cores all

To inspect which external tool commands RNAConSnake is configured to use, and where their executables resolve on the current machine, run:

rnaconsnake-run --show-tool-paths

Structured export can be triggered from the main CLI after a successful workflow run:

rnaconsnake-run \
  --input-alignment /path/to/input.stk \
  --output-dir /path/to/run_dir \
  --export-bundle /path/to/export_bundle \
  --cores all

Tests And Fixtures

The test suite lives in tests/test_python_tools.py.

Fixtures are split into two groups:

  • tests/fixtures: small synthetic fixtures for focused tool behavior
  • tests/fixtures/real: small real-derived fixtures curated from repository input and workflow output data

The real-derived fixtures are intended to stay small enough for CI while still guarding against formatting and behavior regressions in the Stockholm helper tools.

The suite also includes an end-to-end Snakemake smoke test that stubs the external workflow toolchain with temporary fake executables on PATH. That keeps CI independent of the real binaries while still exercising the packaged workflow DAG.

To verify that two completed runs generated and processed the same deterministic candidate set from the same input alignment, run:

python -m rnaconsnake.tools.verify_run_consistency /path/to/run_a /path/to/run_b

This checks:

  • Lalifold/len_*/RC_*_0001.stk
  • split manifests and per-candidate split Stockholm files
  • cleaned alignment manifests and per-candidate files under generated_files/stk

It deliberately does not compare stochastic downstream metrics such as alifoldz z-scores.

RNAConSnake should remain the scientific computation and export layer only. Any future HTML browser UI should remain outside the scope of this repository.

Shipping Model

Current release model:

  • Python package via pyproject.toml
  • Snakemake orchestration
  • root workflow files copied into the package at build time
  • ViennaRNA and legacy post-processing commands as external runtime dependencies

Planned future direction:

  • loosen the hard external dependency on RNALalifold
  • evaluate wrapping ViennaRNA Python bindings directly from Python