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authorzsloan2021-05-25 20:27:33 +0000
committerzsloan2021-06-18 22:07:44 +0000
commitbf0a8cb22c0cc0c1dfe25740f88a4cb159dd0064 (patch)
treecc73094815a6149fbf04c204428361a2289efd0e /gn3
parentd3a4146fd38fc1d372091cecadfcf7c8fb377f3b (diff)
downloadgenenetwork3-bf0a8cb22c0cc0c1dfe25740f88a4cb159dd0064.tar.gz
Fix R/qtl command and the way keyword arguments are passed
Diffstat (limited to 'gn3')
-rw-r--r--gn3/commands.py4
1 files changed, 2 insertions, 2 deletions
diff --git a/gn3/commands.py b/gn3/commands.py
index 255ea1d..14bd295 100644
--- a/gn3/commands.py
+++ b/gn3/commands.py
@@ -35,10 +35,10 @@ def compose_rqtl_cmd(rqtl_wrapper_cmd: str,
rqtl_wrapper_bool_kwargs: list) -> str:
"""Compose a valid R/qtl command given the correct input"""
# Add kwargs with values
- cmd = rqtl_wrapper_cmd + " " + " ".join(
+ cmd = f"Rscript { rqtl_wrapper_cmd } " + " ".join(
[f"--{key} {val}" for key, val in rqtl_wrapper_kwargs.items()])
- # Add boolean kwargs (kwargs without values)
+ # 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])