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-rw-r--r--wqflask/utility/tools.py8
-rw-r--r--wqflask/wqflask/show_trait/show_trait.py14
2 files changed, 14 insertions, 8 deletions
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 907b0d6a..22779739 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -93,6 +93,10 @@ def gemma_command(guess=None):
def plink_command(guess=None):
return valid_bin(get_setting("PLINK_COMMAND",guess))
+def flat_file_exists(subdir):
+ base = get_setting("GENENETWORK_FILES")
+ return valid_path(base+"/"+subdir)
+
def flat_files(subdir=None):
base = get_setting("GENENETWORK_FILES")
if subdir:
@@ -104,6 +108,7 @@ def assert_dir(dir):
raise Exception("ERROR: can not find directory "+dir)
return dir
+
def mk_dir(dir):
if not valid_path(dir):
os.makedirs(dir)
@@ -187,7 +192,8 @@ LOG_BENCH = get_setting_bool('LOG_BENCH')
LOG_FORMAT = "%(message)s" # not yet in use
USE_REDIS = get_setting_bool('USE_REDIS')
USE_GN_SERVER = get_setting_bool('USE_GN_SERVER')
-GENENETWORK_FILES = get_setting_bool('GENENETWORK_FILES')
+
+GENENETWORK_FILES = get_setting('GENENETWORK_FILES')
PYLMM_COMMAND = pylmm_command()
GEMMA_COMMAND = gemma_command()
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 2fd525a5..d9617c7c 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -23,7 +23,7 @@ from basicStatistics import BasicStatisticsFunctions
from pprint import pformat as pf
-from utility.tools import flat_files
+from utility.tools import flat_files, flat_file_exists
from utility.logger import getLogger
logger = getLogger(__name__ )
@@ -162,12 +162,12 @@ class ShowTrait(object):
def get_mapping_methods(self):
'''Only display mapping methods when the dataset group's genotype file exists'''
def check_plink_gemma():
- MAPPING_PATH = flat_files("mapping")
- if (os.path.isfile(MAPPING_PATH+"/"+self.dataset.group.name+".bed") and
- os.path.isfile(MAPPING_PATH+"/"+self.dataset.group.name+".map")):
- return True
- else:
- return False
+ if flat_file_exists("mapping"):
+ MAPPING_PATH = flat_files("mapping")+"/"
+ if (os.path.isfile(MAPPING_PATH+self.dataset.group.name+".bed") and
+ os.path.isfile(MAPPING_PATH+self.dataset.group.name+".map")):
+ return True
+ return False
def check_pylmm_rqtl():
if os.path.isfile(webqtlConfig.GENODIR+self.dataset.group.name+".geno") and (os.path.getsize(webqtlConfig.JSON_GENODIR+self.dataset.group.name+".json") > 0):