diff options
Diffstat (limited to 'gn3/computations/gemma.py')
| -rw-r--r-- | gn3/computations/gemma.py | 26 |
1 files changed, 26 insertions, 0 deletions
diff --git a/gn3/computations/gemma.py b/gn3/computations/gemma.py index ae04c40..5741692 100644 --- a/gn3/computations/gemma.py +++ b/gn3/computations/gemma.py @@ -5,8 +5,11 @@ import string from base64 import b64encode from hashlib import md5 +from typing import Dict from typing import List +from typing import Optional from typing import ValuesView +from gn3.commands import compose_gemma_cmd def generate_random_n_string(n_length: int) -> str: """Generate a random string that is N chars long""" @@ -50,3 +53,26 @@ def do_paths_exist(paths: ValuesView) -> bool: if not os.path.isfile(path): return False 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""" + 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} + if gemma_kwargs.get("covar_filename"): + _kwargs["a"] = gemma_kwargs.get("covar_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_kwargs=_kwargs, + gemma_args=["-gk", ">", + output_file]) |