diff options
| -rw-r--r-- | gn3/computations/gemma.py | 26 | ||||
| -rw-r--r-- | tests/unit/computations/test_gemma.py | 20 |
2 files changed, 46 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]) diff --git a/tests/unit/computations/test_gemma.py b/tests/unit/computations/test_gemma.py index 23707ef..a7884ea 100644 --- a/tests/unit/computations/test_gemma.py +++ b/tests/unit/computations/test_gemma.py @@ -4,6 +4,7 @@ import unittest from unittest import mock 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): @@ -29,3 +30,22 @@ class TestGemma(unittest.TestCase): """Test that a string is hashed correctly""" 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_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")) |