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authorBonfaceKilz2021-03-08 15:26:33 +0300
committerBonfaceKilz2021-03-08 21:09:58 +0300
commit776598729bcff12bea933ff7cb4864e1c3eea0c8 (patch)
tree97a1d4411da82879cd01a025994c84ab67ff61da /gn3/computations
parente5bcb0faccf67f213538cad3670a8d1378c56ce7 (diff)
downloadgenenetwork3-776598729bcff12bea933ff7cb4864e1c3eea0c8.tar.gz
Delete "generate_gemma_computation_cmd"
Diffstat (limited to 'gn3/computations')
-rw-r--r--gn3/computations/gemma.py22
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,