anndict.adata_dict.read_adata_dict

anndict.adata_dict.read_adata_dict(directory)

Read an AdataDict from a previously saved AdataDict. To write an AdataDict see write_adata_dict().

Parameters:

directory str

Base directory where the .h5ad files and hierarchy file are located.

Return type:

AdataDict

Returns:

An AdataDict reconstructed from the saved files.

Raises:

• FileNotFoundError – If the directory or required metadata files don’t exist.

• ValueError – If the metadata files are corrupted or in an unexpected format.

Examples

Case 1: Flat hierarchy

directory/
├── adata_dict.hierarchy.json
├── adata_dict.db.json
├── <file_prefix>Donor1_Tissue1.h5ad
├── <file_prefix>Donor1_Tissue2.h5ad
└── <file_prefix>Donor2_Tissue1.h5ad

The reconstructed AdataDict will be:

print(adata_dict)
> {
>     ("Donor1", "Tissue1"): adata_d1_t1,
>     ("Donor1", "Tissue2"): adata_d1_t2,
>     ("Donor2", "Tissue1"): adata_d2_t1,
> }

Case 2: Nested hierarchy

directory/
├── adata_dict.hierarchy.json
├── adata_dict.db.json
├── Donor1/
│   ├── <file_prefix>Tissue1.h5ad
│   └── <file_prefix>Tissue2.h5ad
└── Donor2/
    └── <file_prefix>Tissue1.h5ad

The reconstructed AdataDict will be:

print(adata_dict)
> {
>     ("Donor1",): {
>         ("Tissue1",): adata_d1_t1,
>         ("Tissue2",): adata_d1_t2,
>     },
>     ("Donor2",): {
>         ("Tissue1",): adata_d2_t1,
>     },
> }

Case 3: Nested hierarchy with multiple indices at the deepest level

directory/
├── adata_dict.hierarchy.json
├── adata_dict.db.json
├── Donor1/
│   ├── <file_prefix>Tissue1_CellType1.h5ad
│   ├── <file_prefix>Tissue1_CellType2.h5ad
│   └── <file_prefix>Tissue2_CellType3.h5ad
└── Donor2/
    └── <file_prefix>Tissue1_CellType1.h5ad

The reconstructed AdataDict will be:

print(adata_dict)
> {
>     ("Donor1",): {
>         ("Tissue1", "CellType1"): adata_d1_t1_c1,
>         ("Tissue1", "CellType2"): adata_d1_t1_c2,
>         ("Tissue2", "CellType3"): adata_d1_t2_c3,
>     },
>     ("Donor2",): {
>         ("Tissue1", "CellType1"): adata_d2_t1_c1,
>     },
> }

See also

write_adata_dict()

To write an AdataDict