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| author | Pjotr Prins | 2018-02-10 08:53:27 +0000 |
|---|---|---|
| committer | Pjotr Prins | 2018-02-10 08:53:27 +0000 |
| commit | 91365baf9ba657f56c19201874cdf60aede75dd1 (patch) | |
| tree | 33f9f0069b177d41423004d6f2eff471b56f273a | |
| parent | b3d9c748008d401ca5b5fa5d60a6a1eff505ee3e (diff) | |
| download | genenetwork2-91365baf9ba657f56c19201874cdf60aede75dd1.tar.gz | |
Fixing GEMMA LOCO
| -rwxr-xr-x | bin/genenetwork2 | 4 | ||||
| -rw-r--r-- | 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: |