From 91365baf9ba657f56c19201874cdf60aede75dd1 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sat, 10 Feb 2018 08:53:27 +0000
Subject: Fixing GEMMA LOCO

---
 wqflask/wqflask/marker_regression/gemma_mapping.py | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index c004983e..68920130 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -3,7 +3,7 @@ import os, math, string, random, json
 from base import webqtlConfig
 from base.trait import GeneralTrait
 from base.data_set import create_dataset
-from utility.tools import flat_files, GEMMA_COMMAND, GEMMA_WRAPPER_COMMAND, TEMPDIR, assert_bin
+from utility.tools import flat_files, GEMMA_COMMAND, GEMMA_WRAPPER_COMMAND, TEMPDIR, assert_bin, assert_file
 
 import utility.logger
 logger = utility.logger.getLogger(__name__ )
@@ -210,8 +210,13 @@ def parse_gemma_output(genofile_name):
 def parse_loco_output(this_dataset, gwa_output_filename):
 
     output_filelist = []
-    with open("{}/gn2/".format(TEMPDIR) + gwa_output_filename + ".json") as data_file:
-       data = json.load(data_file)
+    jsonfn = "{}/gn2/".format(TEMPDIR) + gwa_output_filename + ".json"
+    assert_file(jsonfn)
+    try:
+        with open(jsonfn) as data_file:
+            data = json.load(data_file)
+    except:
+        logger.error("Can not parse "+jsonfn)
 
     files = data['files']
     for file in files:
-- 
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