diff options
Diffstat (limited to 'gn3')
| -rw-r--r-- | gn3/computations/gemma.py | 22 |
1 files changed, 0 insertions, 22 deletions
diff --git a/gn3/computations/gemma.py b/gn3/computations/gemma.py index 3c6bd29..bf8b151 100644 --- a/gn3/computations/gemma.py +++ b/gn3/computations/gemma.py @@ -49,28 +49,6 @@ def do_paths_exist(paths: ValuesView) -> bool: return True -def generate_gemma_computation_cmd( - gemma_cmd: str, gemma_kwargs: Dict[str, str], output_file: str, - gemma_wrapper_kwargs: Dict[str, str]) -> Optional[str]: - """Create a computation cmd""" - geno_filename = gemma_kwargs.get("geno_filename", "") - trait_filename = gemma_kwargs.get("trait_filename") - ext, snps_filename = geno_filename.partition(".")[-1], "" - if geno_filename: - snps_filename = geno_filename.replace(f".{ext}", "") - snps_filename += f"_snps.{ext}" - _kwargs = {"g": geno_filename, "p": trait_filename} - _kwargs["a"] = snps_filename - if not do_paths_exist(_kwargs.values()): # Prevents injection! - return None - if _kwargs.get("lmm"): - _kwargs["lmm"] = gemma_kwargs.get("lmm") - return compose_gemma_cmd(gemma_wrapper_cmd=gemma_cmd, - gemma_wrapper_kwargs=gemma_wrapper_kwargs, - gemma_kwargs=_kwargs, - gemma_args=["-gk", ">", output_file]) - - # pylint: disable=R0913 def generate_gemma_cmd(gemma_cmd: str, output_dir: str, |