mudata-oom
Out-of-memory MuData powered by anndataoom.
Drop-in replacement for mudata.MuData whose per-modality expression matrices
stay on disk. Every API method, every property, every behaviour of upstream
mudata.MuData is preserved — the only difference is that the modalities are
anndataoom.AnnDataOOM objects instead of anndata.AnnData, so reading and
processing million-cell multimodal atlases doesn't blow up your RAM.
import mudataoom as moom
mdata = moom.read_h5mu("cite_seq_1M.h5mu")
# MuDataOOM [out-of-memory · backed]
# mod
# rna : AnnDataOOM 1,200,000 × 24,000
# prot : AnnDataOOM 1,200,000 × 156
# obs : 1,200,000 × 5
# obsm : ['X_mofa']
Why?
mudata.MuData is fine for the joint metadata (a few MB), but each modality
is a full AnnData that loads its X into RAM. For a 1M-cell CITE-seq atlas
(RNA + protein), this means >100 GB. mudataoom keeps each modality's X
on disk and runs single-modality preprocessing (normalize, log1p, scale, PCA)
through anndataoom's lazy / chunked operator chain.
| Dataset | mudata.MuData |
mudataoom |
Saving |
|---|---|---|---|
| CITE-seq 10k (RNA + 156 ADT) | 2.4 GB | ~70 MB | 34x |
| RNA + ATAC 100k cells | ~24 GB | ~1.2 GB | 20x |
| RNA + ATAC 1M cells | ~140 GB (OOM) | ~1.7 GB | 80x+ |
Architecture (no new Rust code)
MuDataOOM (Python; subclasses mudata.MuData)
├── _mod: OrderedDict[str, AnnDataOOM] # per-modality; X stays on disk
├── _obs, _var: pd.DataFrame # joint metadata
├── _obsm, _varm, _obsp, _varp # joint embeddings / graphs
├── _obsmap, _varmap # which modality row backs which joint row
├── _uns, _axis
└── _file: MuDataFileManager # h5mu HDF5 file handle (backed mode)
read_h5mu walks /mod/* inside the source .h5mu, builds one tiny
"virtual" .h5ad per modality whose datasets are HDF5 ExternalLinks back
into the source file — no copying of X — then opens each virtual .h5ad
through anndataoom.read(). The Rust I/O layer streams X chunks straight
from the original .h5mu on demand.
See docs/architecture.md for the full design.
Install
pip install mudataoom
(Will pull anndataoom, mudata, h5py, anndata.)
Compatibility
MuDataOOM is a strict subclass of mudata.MuData. Anything that takes a
mudata.MuData (mofapy, muon plotting, scvi-tools, …) accepts a
MuDataOOM unchanged.
License
MIT. See LICENSE.
Metadata
Release files for mudataoom 0.3.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| mudataoom-0.3.0.tar.gz | 170.7 kB | Details |
Built distributions (wheels)
Total release size: 145.4 MB
Release files / mudataoom-0.3.0.tar.gz
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