From 476b146562070cee6a55c55c03c37ef3e19a1474 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 18 Jun 2021 20:54:18 +0000
Subject: Resolve mypy errors in computations/rqtl.py

---
 gn3/computations/rqtl.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/gn3/computations/rqtl.py b/gn3/computations/rqtl.py
index 22d9faf..7b1a35c 100644
--- a/gn3/computations/rqtl.py
+++ b/gn3/computations/rqtl.py
@@ -1,8 +1,7 @@
 """Procedures related rqtl computations"""
 import os
 import numpy as np
-from typing import Dict
-from typing import List
+from typing import Dict, List, Union
 
 from flask import current_app
 
@@ -55,7 +54,7 @@ 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"), "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:
@@ -63,6 +62,7 @@ def process_rqtl_output(file_name: str) -> List:
                 continue
             else:
                 # Convert chr to int if possible
+                the_chr: Union[int, str]
                 try:
                     the_chr = int(line_items[1][1:-1])
                 except:
@@ -85,7 +85,7 @@ def process_perm_output(file_name: str):
 
     """
     perm_results = []
-    with open(os.path.join(current_app.config.get("TMPDIR"), "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
-- 
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