From 624ece086d026da9150cd35b2404874ccf607b07 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 17 May 2021 21:56:51 +0000
Subject: 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

---
 gn3/commands.py          |  7 +++++++
 gn3/computations/rqtl.py | 25 +++++++++++++++++++++++++
 2 files changed, 32 insertions(+)
 create mode 100644 gn3/computations/rqtl.py

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
-- 
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