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, and
converts to and from 10x, STARsolo, Visium, Xenium, CellBender, Parse, loom, MuData
and more.
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.