Module export 

Write a backend out to the interchange formats scanpy and Seurat read.

• to_mtx: a 10x Genomics Cell Ranger MEX triplet directory (matrix.mtx, features.tsv, barcodes.tsv, gzipped by default), loaded by scanpy.read_10x_mtx(dir) and Seurat Read10X(dir).
• [to_h5ad] (feature hdf5): an AnnData .h5ad file, loaded by anndata.read_h5ad, with optional obs / var metadata tables.

Both take a backend already open, so a caller holding one does not open it again; open_sparse_matrix_by_path opens one from its file. These are what data-beans to-mtx and data-beans to-h5ad run, and write the same bytes.

use data_beans::export::{self, MtxExport};
use data_beans::sparse_io::open_sparse_matrix_by_path;

let data = open_sparse_matrix_by_path("sim.zarr.zip")?;
// sim_mtx/{matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz}
export::to_mtx(data.as_ref(), "sim_mtx", &MtxExport::default())?;

#[cfg(feature = "hdf5")]
{
    let mut data = data;
    let out = export::h5ad_path("sim.zarr.zip", None); // "sim.h5ad"
    export::to_h5ad(data.as_mut(), &out, &export::H5adExport::default())?;
}

Structs

MtxExport

How to_mtx writes the triplet.

Functions

to_mtx

Export data to a 10x Genomics MEX (MatrixMarket) triplet in the directory out_dir, created if missing, readable by scanpy / Seurat. This is the inverse of crate::import::from_mtx; the directory is returned.