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author | zsloan | 2021-06-18 17:33:09 -0500 |
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committer | GitHub | 2021-06-18 17:33:09 -0500 |
commit | d653a635d0efd2291754c18f51d31f91a1c0a25c (patch) | |
tree | 309ea800da204f721e92ebc1c725144eab939d0f /gn3/commands.py | |
parent | c553b52e140de1d7e5ed49f07bae2f4a120266f8 (diff) | |
parent | f7becfa11ca857104ecc1b668b4bd3d0a721083c (diff) | |
download | genenetwork3-d653a635d0efd2291754c18f51d31f91a1c0a25c.tar.gz |
Merge pull request #13 from zsloan/feature/add_rqtl_endpoints
Feature/add rqtl endpoints
Diffstat (limited to 'gn3/commands.py')
-rw-r--r-- | gn3/commands.py | 14 |
1 files changed, 14 insertions, 0 deletions
diff --git a/gn3/commands.py b/gn3/commands.py index 4b0d62d..14bd295 100644 --- a/gn3/commands.py +++ b/gn3/commands.py @@ -30,6 +30,20 @@ def compose_gemma_cmd(gemma_wrapper_cmd: str = "gemma-wrapper", cmd += " ".join([f"{arg}" for arg in gemma_args]) return cmd +def compose_rqtl_cmd(rqtl_wrapper_cmd: str, + rqtl_wrapper_kwargs: Dict, + rqtl_wrapper_bool_kwargs: list) -> str: + """Compose a valid R/qtl command given the correct input""" + # Add kwargs with values + cmd = f"Rscript { rqtl_wrapper_cmd } " + " ".join( + [f"--{key} {val}" for key, val in rqtl_wrapper_kwargs.items()]) + + # Add boolean kwargs (kwargs that are either on or off, like --interval) + if rqtl_wrapper_bool_kwargs: + cmd += " " + cmd += " ".join([f"--{val}" for val in rqtl_wrapper_bool_kwargs]) + + return cmd def queue_cmd(conn: Redis, job_queue: str, |