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authorFrederick Muriuki Muriithi2021-09-22 08:36:11 +0300
committerFrederick Muriuki Muriithi2021-09-22 08:36:11 +0300
commit71cc35e5178904b512b9007e33be17a36f6656f2 (patch)
tree2d059b89aa30ce55d2cafe781915abc3ea31d948 /gn3/computations/qtlreaper.py
parentcd7f301688fd9780df1f842f8bd2b7602775ba1f (diff)
downloadgenenetwork3-71cc35e5178904b512b9007e33be17a36f6656f2.tar.gz
Fix typing issues
* Ignore some errors * Update typing definitions for some portions of code * Add missing imports
Diffstat (limited to 'gn3/computations/qtlreaper.py')
-rw-r--r--gn3/computations/qtlreaper.py6
1 files changed, 4 insertions, 2 deletions
diff --git a/gn3/computations/qtlreaper.py b/gn3/computations/qtlreaper.py
index 5d17fed..5ddea76 100644
--- a/gn3/computations/qtlreaper.py
+++ b/gn3/computations/qtlreaper.py
@@ -4,6 +4,8 @@ computation of QTLs.
"""
import os
import subprocess
+from typing import Union
+
from gn3.random import random_string
from gn3.settings import TMPDIR, REAPER_COMMAND
@@ -70,9 +72,9 @@ def run_reaper(
output_dir, random_string(10))
output_list = ["--main_output", output_filename]
if separate_nperm_output:
- permu_output_filename = "{}/qtlreaper/permu_output_{}.txt".format(
+ permu_output_filename: Union[None, str] = "{}/qtlreaper/permu_output_{}.txt".format(
output_dir, random_string(10))
- output_list = output_list + ["--permu_output", permu_output_filename]
+ output_list = output_list + ["--permu_output", permu_output_filename] # type: ignore[list-item]
else:
permu_output_filename = None