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

2 files changed, 32 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,
diff --git a/gn3/computations/rqtl.py b/gn3/computations/rqtl.py
new file mode 100644
index 0000000..087a99f
--- /dev/null
+++ b/gn3/computations/rqtl.py
@@ -0,0 +1,25 @@
+"""Procedures related rqtl computations"""

+import os

+

+from typing import Dict

+from gn3.commands import compose_rqtl_cmd

+from gn3.fs_helpers import get_hash_of_files

+

+def generate_rqtl_cmd(rqtl_wrapper_cmd: str,

+                      output_dir: str,

+                      rqtl_wrapper_kwargs: Dict) -> Dict:

+

+    _hash = get_hash_of_files(

+        [v for k, v in rqtl_wrapper_kwargs.items() if k in ["g", "p", "addcovar",

+                                                    "model", "method",

+                                                    "interval", "nperm",

+                                                    "scale", "control"]])

+

+    _output_filename = f"{_hash}-output.json"

+    return {

+        "output_file":

+        _output_filename,

+        "rqtl_cmd":

+        compose_rqtl_cmd(rqtl_wrapper_cmd=rqtl_wrapper_cmd,

+                         rqtl_wrapper_kwargs=rqtl_wrapper_kwargs)

+    }
\ No newline at end of file