CAP-AnnData: Partial I/O for AnnData (.h5ad) Files

Overview

CAP-AnnData offering functionalities for selective reading and writing of AnnData file fields without the need for loading entire dataset (or even entire field) into memory. For example, it allows to read and modify the single obs column taking nothing into memory except the column itself. Package eager to replicate the original AnnData API as much as possible, while providing additional features for efficient data manipulation for heavy datasets.

Installation

Install CAP-AnnData via pip:

pip install -U cap-anndata

Basic Example

The example below displayes how to read a single obs column, create new obs column and propagate it to the .h5ad file.

from cap_anndata import read_h5ad

file_path = "your_data.h5ad"
with read_h5ad(file_path=file_path, edit=True) as cap_adata:
    print(cap_adata.obs_keys())  # ['a', 'b', 'c']
    print(cap_adata.obs) # Empty DataFrame
    cap_adata.read_obs(columns=['a'])
    print(cap_adata.obs.columns) # ['a']
    cap_adata.obs['new_col'] = cap_adata.obs['a']
    cap_adata.overwrite(fields=['obs'])

More example can be found in the How-TO file.