Created compose_rqtl_command and generate_rqtl_command to create the actual command to be run from the command line; used the same pattern as for GEMMA for consistency

1 files changed, 7 insertions, 0 deletions

diff --git a/gn3/commands.py b/gn3/commands.py
index 4b0d62d..db32d1f 100644
--- a/gn3/commands.py
+++ b/gn3/commands.py
@@ -30,6 +30,13 @@ 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) -> str:
+    """Compose a valid R/qtl command given the correct input"""
+    cmd = rqtl_wrapper_cmd + " " + " ".join(
+        [f"--{key} {val}" for key, val in rqtl_wrapper_kwargs.items()])
+
+    return cmd
 
 def queue_cmd(conn: Redis,
               job_queue: str,