From d42b85ae5fcea1b71a7165fd6e64745a228c48f9 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 18 Jun 2021 21:13:03 +0000
Subject: Fixed pylint issues

---
 gn3/api/rqtl.py          |  7 ++++---
 gn3/computations/rqtl.py | 45 ++++++++++++++++++++++++---------------------
 2 files changed, 28 insertions(+), 24 deletions(-)

diff --git a/gn3/api/rqtl.py b/gn3/api/rqtl.py
index 38f4c1e..ebb746c 100644
--- a/gn3/api/rqtl.py
+++ b/gn3/api/rqtl.py
@@ -6,7 +6,6 @@ from flask import current_app
 from flask import jsonify
 from flask import request
 
-from gn3.commands import run_cmd
 from gn3.computations.rqtl import generate_rqtl_cmd, process_rqtl_output, process_perm_output
 from gn3.computations.gemma import do_paths_exist
 
@@ -45,13 +44,15 @@ run the rqtl_wrapper script and return the results as JSON
     )
 
     rqtl_output = {}
-    if not os.path.isfile(os.path.join(current_app.config.get("TMPDIR"), "output", rqtl_cmd.get('output_file'))):
+    if not os.path.isfile(os.path.join(current_app.config.get("TMPDIR"),
+                                       "output", rqtl_cmd.get('output_file'))):
         os.system(rqtl_cmd.get('rqtl_cmd'))
 
     rqtl_output['results'] = process_rqtl_output(rqtl_cmd.get('output_file'))
 
     rqtl_output['results'] = process_rqtl_output(rqtl_cmd.get('output_file'))
     if int(rqtl_kwargs['nperm']) > 0:
-        rqtl_output['perm_results'], rqtl_output['suggestive'], rqtl_output['significant'] = process_perm_output(rqtl_cmd.get('output_file'))
+        rqtl_output['perm_results'], rqtl_output['suggestive'], rqtl_output['significant'] = \
+        process_perm_output(rqtl_cmd.get('output_file'))
 
     return jsonify(rqtl_output)
diff --git a/gn3/computations/rqtl.py b/gn3/computations/rqtl.py
index 7b1a35c..0433b3f 100644
--- a/gn3/computations/rqtl.py
+++ b/gn3/computations/rqtl.py
@@ -1,8 +1,9 @@
 """Procedures related rqtl computations"""
 import os
-import numpy as np
 from typing import Dict, List, Union
 
+import numpy as np
+
 from flask import current_app
 
 from gn3.commands import compose_rqtl_cmd
@@ -54,27 +55,28 @@ def process_rqtl_output(file_name: str) -> List:
     marker_obs = []
     # Later I should probably redo this using csv.read to avoid the
     # awkwardness with removing quotes with [1:-1]
-    with open(os.path.join(current_app.config.get("TMPDIR", "/tmp"), "output", file_name), "r") as the_file:
+    with open(os.path.join(current_app.config.get("TMPDIR", "/tmp"),
+                           "output", file_name), "r") as the_file:
         for line in the_file:
             line_items = line.split(",")
             if line_items[1][1:-1] == "chr" or not line_items:
                 # Skip header line
                 continue
-            else:
-                # Convert chr to int if possible
-                the_chr: Union[int, str]
-                try:
-                    the_chr = int(line_items[1][1:-1])
-                except:
-                    the_chr = line_items[1][1:-1]
-                this_marker = {
-                    "name": line_items[0][1:-1],
-                    "chr": the_chr,
-                    "cM": float(line_items[2]),
-                    "Mb": float(line_items[2]),
-                    "lod_score": float(line_items[3])
-                }
-                marker_obs.append(this_marker)
+
+            # Convert chr to int if possible
+            the_chr: Union[int, str]
+            try:
+                the_chr = int(line_items[1][1:-1])
+            except ValueError:
+                the_chr = line_items[1][1:-1]
+            this_marker = {
+                "name": line_items[0][1:-1],
+                "chr": the_chr,
+                "cM": float(line_items[2]),
+                "Mb": float(line_items[2]),
+                "lod_score": float(line_items[3])
+            }
+            marker_obs.append(this_marker)
 
     return marker_obs
 
@@ -85,14 +87,15 @@ def process_perm_output(file_name: str):
 
     """
     perm_results = []
-    with open(os.path.join(current_app.config.get("TMPDIR", "/tmp"), "output", "PERM_" + file_name), "r") as the_file:
+    with open(os.path.join(current_app.config.get("TMPDIR", "/tmp"),
+                           "output", "PERM_" + file_name), "r") as the_file:
         for i, line in enumerate(the_file):
             if i == 0:
                 # Skip header line
                 continue
-            else:
-                line_items = line.split(",")
-                perm_results.append(float(line_items[1]))
+
+            line_items = line.split(",")
+            perm_results.append(float(line_items[1]))
 
     suggestive = np.percentile(np.array(perm_results), 67)
     significant = np.percentile(np.array(perm_results), 95)
-- 
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