aboutsummaryrefslogtreecommitdiff
path: root/wqflask
diff options
context:
space:
mode:
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/base/webqtlConfig.py1
-rw-r--r--wqflask/utility/tools.py13
-rw-r--r--wqflask/wqflask/marker_regression/gemma_mapping.py16
3 files changed, 17 insertions, 13 deletions
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index 1ef2bc26..1e66e957 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -82,6 +82,7 @@ assert_writable_dir(GENERATED_TEXT_DIR)
# Flat file directories
GENODIR = flat_files('genotype')+'/'
assert_dir(GENODIR)
+assert_dir(GENODIR+'bimbam') # for gemma
# JSON genotypes are OBSOLETE
JSON_GENODIR = flat_files('genotype/json')+'/'
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 57f97a81..d3113302 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -16,7 +16,7 @@ OVERRIDES = {}
def app_set(command_id, value):
"""Set application wide value"""
app.config.setdefault(command_id,value)
- value
+ return value
def get_setting(command_id,guess=None):
"""Resolve a setting from the environment or the global settings in
@@ -51,7 +51,7 @@ def get_setting(command_id,guess=None):
return None
# ---- Check whether environment exists
- logger.debug("Looking for "+command_id+"\n")
+ # print("Looking for "+command_id+"\n")
command = value(os.environ.get(command_id))
if command is None or command == "":
command = OVERRIDES.get(command_id)
@@ -63,7 +63,7 @@ def get_setting(command_id,guess=None):
if command is None or command == "":
# print command
raise Exception(command_id+' setting unknown or faulty (update default_settings.py?).')
- logger.debug("Set "+command_id+"="+str(command))
+ # print("Set "+command_id+"="+str(command))
return command
def get_setting_bool(id):
@@ -253,6 +253,7 @@ JS_GN_PATH = get_setting('JS_GN_PATH')
PYLMM_COMMAND = app_set("PYLMM_COMMAND",pylmm_command())
GEMMA_COMMAND = app_set("GEMMA_COMMAND",gemma_command())
+assert(GEMMA_COMMAND is not None)
PLINK_COMMAND = app_set("PLINK_COMMAND",plink_command())
GEMMA_WRAPPER_COMMAND = gemma_wrapper_command()
TEMPDIR = tempdir() # defaults to UNIX TMPDIR
@@ -266,7 +267,7 @@ from six import string_types
if os.environ.get('WQFLASK_OVERRIDES'):
jsonfn = get_setting('WQFLASK_OVERRIDES')
- logger.error("WQFLASK_OVERRIDES: %s" % jsonfn)
+ logger.info("WQFLASK_OVERRIDES: %s" % jsonfn)
with open(jsonfn) as data_file:
overrides = json.load(data_file)
for k in overrides:
@@ -278,8 +279,4 @@ if os.environ.get('WQFLASK_OVERRIDES'):
logger.debug(OVERRIDES)
# assert_file(PHEWAS_FILES+"/auwerx/PheWAS_pval_EMMA_norm.RData")
-# assert_dir(get_setting("JS_BIODALLIANCE"))
-# assert_file(get_setting("JS_BIODALLIANCE")+"/build/dalliance-all.js")
-# assert_file(get_setting("JS_BIODALLIANCE")+"/build/worker-all.js")
-# assert_dir(get_setting("JS_TWITTER_POST_FETCHER"))
assert_file(JS_TWITTER_POST_FETCHER_PATH+"/js/twitterFetcher_min.js")
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index a24e43d4..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
+from utility.tools import flat_files, GEMMA_COMMAND, GEMMA_WRAPPER_COMMAND, TEMPDIR, assert_bin, assert_file
import utility.logger
logger = utility.logger.getLogger(__name__ )
@@ -11,6 +11,7 @@ logger = utility.logger.getLogger(__name__ )
def run_gemma(this_dataset, samples, vals, covariates, method, use_loco):
"""Generates p-values for each marker using GEMMA"""
+ assert_bin(GEMMA_COMMAND);
if this_dataset.group.genofile != None:
genofile_name = this_dataset.group.genofile[:-5]
else:
@@ -27,7 +28,7 @@ def run_gemma(this_dataset, samples, vals, covariates, method, use_loco):
if i < (len(this_chromosomes) - 1):
chr_list_string += this_chromosomes[i+1].name + ","
else:
- chr_list_string += this_chromosomes[i+1].name
+ chr_list_string += this_chromosomes[i+1].name
if covariates != "":
gen_covariates_file(this_dataset, covariates)
@@ -209,8 +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:
@@ -247,4 +253,4 @@ def parse_loco_output(this_dataset, gwa_output_filename):
included_markers.append(line.split("\t")[1])
p_values.append(float(line.split("\t")[10]))
- return marker_obs \ No newline at end of file
+ return marker_obs