adata-cli

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/

Quick start

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.h5ad

The 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

Documentation

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/.

Repository

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

Changes

See the changelog.

Licence

MIT