aboutsummaryrefslogtreecommitdiff
path: root/wqflask
diff options
context:
space:
mode:
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/utility/tools.py5
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression.py13
2 files changed, 8 insertions, 10 deletions
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 51189fa3..b8eff12a 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -1,4 +1,3 @@
-
# Tools/paths finder resolves external paths from settings and/or environment
# variables
@@ -105,9 +104,9 @@ def locate(name, subdir=None):
print("Found: file "+lookfor+"\n")
return lookfor
else:
- raise IOError("Can not locate "+lookfor)
+ raise Exception("Can not locate "+lookfor)
if subdir: sys.stderr.write(subdir)
- raise IOError("Can not locate "+name+" in "+base)
+ raise Exception("Can not locate "+name+" in "+base)
def locate_ignore_error(name, subdir=None):
"""
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 910d0c3c..e9cfb06d 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -41,7 +41,8 @@ from wqflask.marker_regression import gemma_mapping
#from wqflask.marker_regression import plink_mapping
#from wqflask.marker_regression import rqtl_mapping
-from utility.tools import locate, PYLMM_COMMAND, GEMMA_COMMAND, PLINK_COMMAND
+from utility.tools import locate, locate_ignore_error, PYLMM_COMMAND, GEMMA_COMMAND, PLINK_COMMAND
+from utility.external import shell
class MarkerRegression(object):
@@ -413,8 +414,8 @@ class MarkerRegression(object):
write_cross = ro.r["write.cross"] # Map the write.cross function
GENOtoCSVR = ro.r["GENOtoCSVR"] # Map the GENOtoCSVR function
- genofilelocation = webqtlConfig.HTMLPATH + "genotypes/" + self.dataset.group.name + ".geno"
- crossfilelocation = webqtlConfig.HTMLPATH + "genotypes/" + self.dataset.group.name + ".cross"
+ genofilelocation = locate(self.dataset.group.name + ".geno", "genotype")
+ crossfilelocation = locate(self.dataset.group.name + ".cross", "genotype")
#print("Conversion of geno to cross at location:", genofilelocation, " to ", crossfilelocation)
@@ -860,9 +861,7 @@ class MarkerRegression(object):
Redis.expire(key, 60*60)
command = PYLMM_COMMAND+' --key {} --species {}'.format(key,"other")
-
- os.system(command)
-
+ shell(command)
json_results = Redis.blpop("pylmm:results:" + temp_uuid, 45*60)
results = json.loads(json_results[1])
@@ -941,7 +940,7 @@ class MarkerRegression(object):
print("command is:", command)
print("after printing command")
- os.system(command)
+ shell(command)
#t_stats, p_values = lmm.run(key)
#lmm.run(key)