import os
import subprocess
[docs]def run_h5ad_rds(input_anndata, output_rds):
"""
Convert a .h5ad file to a Seurat RDS object by calling an R script.
Parameters
----------
input_anndata : str
Path to the input .h5ad file to be converted.
output_rds : str
Path where the resulting .rds file will be saved.
Returns
-------
None
The Seurat object is saved to the location specified by output_rds.
"""
script_dir = os.path.dirname(os.path.abspath(__file__))
r_script = os.path.join(script_dir, "r_convert.R")
if not os.path.exists(r_script):
raise FileNotFoundError(f"Cannot find R script at: {r_script}")
subprocess.run(["Rscript", r_script, input_anndata, output_rds], check=True)