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

---
 bin/genenetwork2                                   |  4 +++-
 wqflask/wqflask/marker_regression/gemma_mapping.py | 11 ++++++++---
 2 files changed, 11 insertions(+), 4 deletions(-)

diff --git a/bin/genenetwork2 b/bin/genenetwork2
index 7148c022..52144f4d 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -121,7 +121,9 @@ else
     export PLINK_COMMAND="$GN2_PROFILE/bin/plink2"
     export PYLMM_COMMAND="$GN2_PROFILE/bin/pylmm_redis"
     export GEMMA_COMMAND="$GN2_PROFILE/bin/gemma"
-    export GEMMA_WRAPPER_COMMAND="$GN2_PROFILE/bin/gemma-wrapper"
+    if [ -z GEMMA_WRAPPER_COMMAND ]; then
+        export GEMMA_WRAPPER_COMMAND="$GN2_PROFILE/bin/gemma-wrapper"
+    fi
     if [ ! -d $PYTHONPATH ] ; then echo "PYTHONPATH not valid "$PYTHONPATH ; exit 1 ; fi
     if [ ! -d $R_LIBS_SITE ] ; then echo "R_LIBS_SITE not valid "$R_LIBS_SITE ; exit 1 ; fi
     if [ ! -d $GEM_PATH ] ; then echo "GEM_PATH not valid "$GEM_PATH ; exit 1 ; fi
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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