quadrat

Sequence-to-function training data, straight from BAM.

A quadrat is the fixed-size frame a field ecologist drops on the ground to tally everything inside it, moved across a landscape by a sampling design chosen separately from the frame. This package is that: a fixed-length window, placed at loci by a sampling scheme, tallying the cut sites that fall inside.

Everything between a set of alignments and a batch of (sequence, signal) pairs is independent of the model that consumes them. quadrat implements that span — the pileup, the window cache, the sampler and the loader — so any sequence-to-function architecture can be trained without reimplementing it.

Status

Under construction. The data path is being extracted from cherimoya; see #1 for the specification and the slices it lands in.

Install

Nothing is published yet. Once the data path lands, the two installs will be:

pip install quadrat            # stream windows over cut-site tables
pip install "quadrat[pileup]"  # also build those tables from alignments

The pileup extra adds the engine that builds those tables: polars-bio and giql among its dependencies. The base install is enough for a caller who already has cut-site tables; quadrat's package docstring states the import guarantee that makes it so.

The extra resolves with uv and not yet with pip, because one of its dependencies is pinned to a git revision that only uv reads — the comment on [tool.uv.sources] in pyproject.toml says why and when that changes.

Development

uv sync --locked --all-extras                     # install, pileup engine included
uv run pytest -q                                  # run the suite
uv run ruff format --check src tests build-hooks   # check formatting
uv run ruff check src tests build-hooks            # lint

The version is the repository's rather than a literal in the tree: a vMAJOR.MINOR.PATCH tag names a release, and a commit between tags reports the last release plus the commit it is, so releasing is pushing a tag and nothing in the tree changes for one. A build from a tree that is not a checkout — an unpacked source distribution — reports the version that distribution was built with.

uv sync --locked --no-dev installs what pip install quadrat will, which is the base install the import guarantee above is about; CI runs it as a job of its own.

License

MIT.