def run_r_script_logged(branch: "CellBranch", r_script_filepath: str,
arg_list: list, logfile_prefix: str):
"""
Runs an R script for a process, which additionally entails outputting log
files
"""
command_string = f"Rscript {r_script_filepath} {' '.join(map(str, arg_list))}"
process_run = branch[branch.current_process]
logs_dir = str(process_run.logs_path)
process_shell_command(command_string, logs_dir, logfile_prefix)
def run_process_r_script(forest: "CellForest", r_script_filepath: str,
arg_list: list, process_name: str):
"""
Runs an R script for a process, which additionally entails outputting log
files
"""
command_string = f"Rscript {r_script_filepath} {' '.join(map(str, arg_list))}"
working_dir = str(forest[process_name].path)
process_shell_command(
command_string=command_string,
working_dir=working_dir,
process_name=process_name,
)
def old_rds_to_pickle(rds_path, output_dir):
output_dir = Path(output_dir)
if not os.path.isfile(rds_path):
raise ValueError(f"rds file does not exists: {rds_path}")
output_mtx_path = output_dir / "matrix.mtx"
output_pickle_path = output_dir / "matrix.pickle"
output_cell_ids_path = output_dir / "cell_ids.tsv"
output_genes_path = output_dir / "genes.tsv"
output_metadata_path = output_dir / "cell_metadata.tsv"
cmd_str = f"Rscript {RDS_CONVERTER_SCRIPT} {rds_path} {output_mtx_path} {output_cell_ids_path} {output_genes_path} {output_metadata_path}"
process_shell_command(cmd_str, output_dir, "matrix_rds_to_sparse_pickle")
sparse_matrix = mmread(str(output_mtx_path)).T.tocsr()
with open(str(output_pickle_path), "wb") as f:
pickle.dump(sparse_matrix, f, protocol=pickle.HIGHEST_PROTOCOL)
paths_to_zip = [output_mtx_path, output_cell_ids_path, output_genes_path]
for filepath in paths_to_zip:
gzip_replace(filepath)
def _run_r_script(script_path: str, working_dir: Union[str, Path],
arg_list: list, process_name: str):
command_string = f"Rscript {str(script_path)} {' '.join(map(str, arg_list))}"
process_shell_command(command_string=command_string,
logs_dir=working_dir,
logfile_prefix=process_name)