Contents

ALLCools.count_matrix.snap

ALLCools.count_matrix.snap

Module Contents

SNAP_BD_FIELDS[source]
read_snap(file_path, bin_kind=5000)[source]

Read snap hdf5 file into anndata.AnnData.

_read_snap_meta(f)[source]
_read_snap_genes(file_path)[source]

Read gene data from snap hdf5 file into anndata.AnnData

_read_snap_bins(file_path, bin_size=5000)[source]

Read bin data from snap hdf5 file into anndata.AnnData

adata_to_df(adata, var_dim, obs_dim='cell', dtype=np.uint8)[source]
snap_to_xarray(snap_path, bin_sizes=(5000,), gene=True, dtype=np.uint8)[source]
snap_to_zarr(snap_path, output_path, bin_sizes=(5000,), gene=True, dtype=np.uint8, index_prefix=None)[source]

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