Explore and edit huge AnnData stores (.h5ad and .zarr) from the command line,
without loading them into memory and without a Python session. adata inspects,
subsets, splits, concatenates, recasts and converts stores, and moves elements in
and out as CSV, JSON, .npy, .mtx or images. It implements the AnnData on-disk
spec directly against h5py and zarr, so it streams stores larger than RAM. It
reads 10x, STARsolo, Visium, Xenium, CellBender, Parse, loom, MuData and more,
and writes 10x, loom and MuData.
Documentation: https://cellgeni.github.io/adata-cli/
pip install pyadata-cli
adata view data.h5ad
adata subset data.h5ad -o cortex.h5ad --obs-query "cluster == Cortex_2"
adata convert filtered_feature_bc_matrix.h5 -o counts.h5adThe command is adata; the distribution is pyadata-cli, because adata-cli was
taken on PyPI. pip install 'pyadata-cli[pickle]' adds pycisTopic pickles, and
'pyadata-cli[spatial]' Visium HD. The container image, with both, is
quay.io/cellgeni/adata-cli:
docker run --rm -v "$PWD":/data quay.io/cellgeni/adata-cli:latest adata view /data/data.h5ad| Page | |
|---|---|
| Getting started | Install, then a first session: inspect, export, subset, import, convert |
| Guides | Inspect and export, subset and split, concatenate, recast, convert formats, pipelines and containers |
| Reference | Every command and flag, each format, query expressions, the on-disk spec, benchmarks |
| Troubleshooting | Error messages and their fixes |
| Developers | Layout, layers, the rules the code relies on, tests, releases |
The pages are also readable on GitHub in docs/.
| Path | Contents |
|---|---|
src/adata/cli.py, commands/ |
The command-line app, and one module per command |
src/adata/core/ |
The streaming algorithms: subset, concat, recast, the out-of-core transpose, queries |
src/adata/elements/, storage/ |
The AnnData on-disk spec, over h5py and zarr alike |
src/adata/conversion/, formats/ |
convert's formats, and the file types of export and import |
tests/ |
The test suite, including anndata compatibility and complexity guards |
benchmarks/ |
The comparison against anndata and scanpy, rerun on every release |
docs/ |
Documentation site |
Dockerfile |
The quay.io/cellgeni/adata-cli image |
.github/workflows/ |
Tests, PyPI and image publishing, benchmarks |
See the changelog.