diff options
Diffstat (limited to 'gn3/computations')
| -rw-r--r-- | gn3/computations/gemma.py | 14 |
1 files changed, 8 insertions, 6 deletions
diff --git a/gn3/computations/gemma.py b/gn3/computations/gemma.py index 5741692..528f888 100644 --- a/gn3/computations/gemma.py +++ b/gn3/computations/gemma.py @@ -55,10 +55,12 @@ 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) -> Optional[str]: - """Create a higher order function that generates a command""" +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], "" @@ -66,13 +68,13 @@ def generate_gemma_computation_cmd(gemma_cmd: str, snps_filename = geno_filename.replace(f".{ext}", "") snps_filename += f"_snps.{ext}" _kwargs = {"g": geno_filename, "p": trait_filename} - if gemma_kwargs.get("covar_filename"): - _kwargs["a"] = gemma_kwargs.get("covar_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]) |