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 +++++++
 1 file changed, 7 insertions(+)

(limited to 'gn3/commands.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,
-- 
cgit v1.2.3


From e61aa16f0bc3dd282060585e655e497fa3d06b49 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 18 May 2021 19:41:01 +0000
Subject: Account for boolean kwargs in compose_rqtl_cmd

---
 gn3/commands.py | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

(limited to 'gn3/commands.py')

diff --git a/gn3/commands.py b/gn3/commands.py
index db32d1f..add715c 100644
--- a/gn3/commands.py
+++ b/gn3/commands.py
@@ -31,11 +31,18 @@ def compose_gemma_cmd(gemma_wrapper_cmd: str = "gemma-wrapper",
     return cmd
 
 def compose_rqtl_cmd(rqtl_wrapper_cmd: str,
-                     rqtl_wrapper_kwargs: Dict) -> 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 = rqtl_wrapper_cmd + " " + " ".join(
         [f"--{key} {val}" for key, val in rqtl_wrapper_kwargs.items()])
 
+    # Add boolean kwargs (kwargs without values)
+    if len(rqtl_wrapper_bool_kwargs):
+        cmd += " "
+        cmd += " ".join([f"--{val}" for val in rqtl_wrapper_bool_kwargs])
+
     return cmd
 
 def queue_cmd(conn: Redis,
-- 
cgit v1.2.3


From 36365588d95d96458da02090ebef21a02366784a Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 18 May 2021 19:49:44 +0000
Subject: Removed len from this if statement, since an empty list evaluates to
 False by itself

---
 gn3/commands.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gn3/commands.py')

diff --git a/gn3/commands.py b/gn3/commands.py
index add715c..255ea1d 100644
--- a/gn3/commands.py
+++ b/gn3/commands.py
@@ -39,7 +39,7 @@ def compose_rqtl_cmd(rqtl_wrapper_cmd: str,
         [f"--{key} {val}" for key, val in rqtl_wrapper_kwargs.items()])
 
     # Add boolean kwargs (kwargs without values)
-    if len(rqtl_wrapper_bool_kwargs):
+    if rqtl_wrapper_bool_kwargs:
         cmd += " "
         cmd += " ".join([f"--{val}" for val in rqtl_wrapper_bool_kwargs])
 
-- 
cgit v1.2.3


From bf0a8cb22c0cc0c1dfe25740f88a4cb159dd0064 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 25 May 2021 20:27:33 +0000
Subject: Fix R/qtl command and the way keyword arguments are passed

---
 gn3/commands.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gn3/commands.py')

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])
-- 
cgit v1.2.3