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| author | BonfaceKilz | 2021-03-10 14:59:25 +0300 |
|---|---|---|
| committer | BonfaceKilz | 2021-03-10 14:59:25 +0300 |
| commit | 8478bc9ee572224fe3b76696de85d1c9a7a89399 (patch) | |
| tree | b12542a1404b58a5cf05a9b63c4bbdb3990b394c | |
| parent | 9170e293e896d1d283d3b19d79d673c9a92724d2 (diff) | |
| download | genenetwork3-8478bc9ee572224fe3b76696de85d1c9a7a89399.tar.gz | |
Fix k-compute command when "loco" is true
| -rw-r--r-- | gn3/computations/gemma.py | 2 | ||||
| -rw-r--r-- | tests/integration/test_gemma.py | 6 | ||||
| -rw-r--r-- | tests/unit/computations/test_gemma.py | 2 |
3 files changed, 5 insertions, 5 deletions
diff --git a/gn3/computations/gemma.py b/gn3/computations/gemma.py index 172333c..5f9d5a3 100644 --- a/gn3/computations/gemma.py +++ b/gn3/computations/gemma.py @@ -59,7 +59,7 @@ def generate_gemma_cmd(gemma_cmd: str, _hash = get_hash_of_files( [v for k, v in gemma_kwargs.items() if k in ["g", "p", "a", "c"]]) if chromosomes: # Only reached when calculating k-values - gemma_wrapper_kwargs = {"loco": f"--input {chromosomes}"} + gemma_wrapper_kwargs = {"loco": f"{chromosomes}"} _hash += f"-{generate_hash_of_string(chromosomes)[:6]}" _output_filename = f"{_hash}-output.json" return { diff --git a/tests/integration/test_gemma.py b/tests/integration/test_gemma.py index 7a7f520..73c7baa 100644 --- a/tests/integration/test_gemma.py +++ b/tests/integration/test_gemma.py @@ -110,7 +110,7 @@ class GemmaAPITest(unittest.TestCase): email=None, job_queue='GN3::job-queue', cmd=("gemma-wrapper --json --loco " - "--input 1,2,3,4,5,6 -- " + "1,2,3,4,5,6 -- " "-g /tmp/test-data/genofile.txt " "-p /tmp/test-data/phenofile.txt " "-a /tmp/test-data/snpfile.txt " @@ -435,7 +435,7 @@ class GemmaAPITest(unittest.TestCase): conn=_redis_conn, email=None, job_queue='GN3::job-queue', - cmd=("gemma-wrapper --json --loco --input 1,2,3,4 -- " + cmd=("gemma-wrapper --json --loco 1,2,3,4 -- " "-g /tmp/my-token/genofile.txt " "-p /tmp/my-token/phenofile.txt " "-a /tmp/my-token/snpfile.txt " @@ -490,7 +490,7 @@ class GemmaAPITest(unittest.TestCase): conn=_redis_conn, email=None, job_queue='GN3::job-queue', - cmd=("gemma-wrapper --json --loco --input 1,2,3,4 -- " + cmd=("gemma-wrapper --json --loco 1,2,3,4 -- " "-g /tmp/my-token/genofile.txt " "-p /tmp/my-token/phenofile.txt " "-a /tmp/my-token/snpfile.txt " diff --git a/tests/unit/computations/test_gemma.py b/tests/unit/computations/test_gemma.py index f3b31e5..1081d12 100644 --- a/tests/unit/computations/test_gemma.py +++ b/tests/unit/computations/test_gemma.py @@ -69,7 +69,7 @@ class TestGemma(unittest.TestCase): "output_file": "my-hash-r+gF5a-output.json", "gemma_cmd": ("gemma-wrapper --json " - "--loco --input 1,2,3,4,5 " + "--loco 1,2,3,4,5 " "-- -g genofile " "-p phenofile -a snpsfile " "-gk > /tmp/my-token/" |