Fixed variety of issues detected by pylint

1 files changed, 25 insertions, 25 deletions

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)
+    }