From 776598729bcff12bea933ff7cb4864e1c3eea0c8 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 8 Mar 2021 15:26:33 +0300
Subject: Delete "generate_gemma_computation_cmd"

---
 gn3/computations/gemma.py | 22 ----------------------
 1 file changed, 22 deletions(-)

(limited to 'gn3')

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,
-- 
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