AnnData Example (https://anndata.readthedocs.io/ based on https://anndata-tutorials.readthedocs.io/en/latest/getting-started.html)

anndata_example.py

import numpy as np
import pandas as pd
import anndata as ad

# Generate example data and build AnnData object
vals = np.random.rand(5, 10).astype('f')
adata = ad.AnnData(vals)

adata
adata.X

adata.obs_names = [f"cell_{i:d}" for i in range(adata.n_obs)]
adata.var_names = [f"gene_symbol_{i:d}" for i in range(adata.n_vars)]

print(adata.obs_names[:3])

tmp = np.random.choice(["cell1", "cell2", "cell3"], size=(adata.n_obs,))
adata.obs["cell_type1_id"] = tmp
adata.obs

tmp = np.random.choice(["cell_type1", "cell_type2", "cell_type3"], size=(adata.n_obs,))
adata.obs["cell_type2_id"] = tmp
adata.obs

tmp = np.random.choice(["G1", "G2", "G3"], size=(adata.n_vars,))
adata.var["gene_type1_id"] = tmp
adata.var

tmp = np.random.choice(["gene_type1", "gene_type2", "gene_type3"], size=(adata.n_vars,))
adata.var["gene_type2_id"] = tmp
adata.var

bdata = adata[adata.obs.cell_type1_id == "cell1"]
bdata

# Write tables
adata.write_csvs("output", skip_data=False)

# Write h5ad format 
adata.write(filename="anndata.h5ad")

# Read data 
cdata = ad.read_h5ad(filename="anndata.h5ad")
cdata

obs.csv

var.csv

X.csv