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-rw-r--r--gn3/computations/gemma.py22
-rw-r--r--tests/unit/computations/test_gemma.py21
2 files changed, 0 insertions, 43 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,
diff --git a/tests/unit/computations/test_gemma.py b/tests/unit/computations/test_gemma.py
index 4a76bef..f3b31e5 100644
--- a/tests/unit/computations/test_gemma.py
+++ b/tests/unit/computations/test_gemma.py
@@ -5,7 +5,6 @@ from unittest import mock
from gn3.computations.gemma import generate_gemma_cmd
from gn3.computations.gemma import generate_hash_of_string
from gn3.computations.gemma import generate_pheno_txt_file
-from gn3.computations.gemma import generate_gemma_computation_cmd
class TestGemma(unittest.TestCase):
@@ -32,26 +31,6 @@ class TestGemma(unittest.TestCase):
self.assertEqual(generate_hash_of_string("I^iQP&TlSR^z"),
"hMVRw8kbEp49rOmoIkhMjA")
- @mock.patch("gn3.computations.gemma.do_paths_exist")
- def test_compose_k_computation_cmd(self, mock_pathsp):
- """Test that a K computation cmd is constructed properly"""
- mock_pathsp.return_value = True
- self.assertEqual(
- generate_gemma_computation_cmd(
- gemma_cmd="gemma-wrapper",
- gemma_wrapper_kwargs=None,
- gemma_kwargs={
- "geno_filename": "genofile.txt",
- "trait_filename": "test.txt",
- "covar_filename": "genofile_snps.txt"
- },
- output_file="/tmp/gn2/k_output_gUFhGu4rLG7k+CXLPk1OUg.txt",
- ), ("gemma-wrapper --json -- "
- "-g genofile.txt -p "
- "test.txt -a genofile_snps.txt "
- "-gk > /tmp/gn2/"
- "k_output_gUFhGu4rLG7k+CXLPk1OUg.txt"))
-
@mock.patch("gn3.computations.gemma.get_hash_of_files")
def test_compute_k_values_without_loco(self, mock_get_hash):
"""Test computing k valuse without loco"""