From 0a8754a582f057bd335441eab15da3f629df9ad7 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 17 May 2021 23:56:10 +0000
Subject: Fixed variety of issues detected by pylint

---
 gn3/computations/rqtl.py | 50 ++++++++++++++++++++++++------------------------
 1 file changed, 25 insertions(+), 25 deletions(-)

(limited to 'gn3/computations/rqtl.py')

diff --git a/gn3/computations/rqtl.py b/gn3/computations/rqtl.py
index 087a99f..0e8cd1f 100644
--- a/gn3/computations/rqtl.py
+++ b/gn3/computations/rqtl.py
@@ -1,25 +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
+"""Procedures related rqtl computations"""
+
+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,
+                      rqtl_wrapper_kwargs: Dict) -> Dict:
+    """Given the base rqtl_wrapper command and
+dict of keyword arguments, return the full rqtl_wrapper command and an
+output filename generated from a hash of the genotype and phenotype files
+
+    """
+
+    _hash = get_hash_of_files(
+        [v for k, v in rqtl_wrapper_kwargs.items() if k in ["g", "p"]])
+
+    _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)
+    }
-- 
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