h5ad CLI

h5ad is a Typer-powered command-line tool for exploring huge .h5ad (AnnData) files without loading them fully into memory. It streams data directly from disk so you can inspect structure, metadata, and matrices on demand.

Features

• info – Reports n_obs × n_var dimensions and highlights top-level groups with their child keys.
• table – Exports obs or var metadata tables to CSV in memory-efficient chunks.
• Colored Rich output for clearer, more informative summaries.

Usage

Install dependencies with uv sync, then invoke any subcommand via uv run h5ad ...:

uv sync
uv run h5ad --help

Examples

Inspect overall structure and axis sizes:

uv run h5ad info data.h5ad

Export full obs metadata to CSV:

uv run h5ad table data.h5ad --axis obs --out obs_metadata.csv

Export selected obs columns to stdout:

uv run h5ad table data.h5ad --axis obs --cols cell_type,donor

Export var metadata with custom chunk size:

uv run h5ad table data.h5ad --axis var --chunk-rows 5000 --out var_metadata.csv

Each command streams from disk, so even multi-GB .h5ad files remain responsive.