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authorzsloan2015-07-09 19:29:30 +0000
committerzsloan2015-07-09 19:29:30 +0000
commit83ff8ce678f15f2f6003a5800a75166544d7c6fa (patch)
tree63af8dcc71f4f2709ac2af2029a7471fd46597dc /wqflask/base
parent25b1d4c4aad2d44e0ff6bfa5aade1783b7a63120 (diff)
downloadgenenetwork2-83ff8ce678f15f2f6003a5800a75166544d7c6fa.tar.gz
Mapping methods now check for existing genotype files.
Currently we still usually get our samplelists from the genofile. This is dumb because it results in us having a bunch of "dummy" genofiles for certain data sets (seems to be mostly human ones). This means that checking for the genofile alone isn't enough to determine if a mapping method should exist for a given group I wrote some code that will instead get the samplelist from the plink .fam file for some of these groups/datasets (if the .fam file exists). Ideally I would like to remove all of the dummy .geno files, but we can't yet do so because it's currently the only place we seem to be storing the sample list for some groups. I also moved gemma into the plink directory to get it out of the git tree. Since it uses the same files as plink, it doesn't make sense for it to be in its own separate directory
Diffstat (limited to 'wqflask/base')
-rwxr-xr-xwqflask/base/data_set.py17
-rwxr-xr-xwqflask/base/webqtlConfig.py2
2 files changed, 14 insertions, 5 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 36f7d036..414cc71a 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -371,7 +371,7 @@ class DatasetGroup(object):
self.parlist = [maternal, paternal]
def get_samplelist(self):
- key = "samplelist:v4:" + self.name
+ key = "samplelist:v2:" + self.name
print("key is:", key)
with Bench("Loading cache"):
result = Redis.get(key)
@@ -384,9 +384,18 @@ class DatasetGroup(object):
print(" self.samplelist: ", self.samplelist)
else:
print("Cache not hit")
- try:
- self.samplelist = get_group_samplelists.get_samplelist(self.name + ".geno")
- except IOError:
+
+ from utility.tools import plink_command
+ PLINK_PATH,PLINK_COMMAND = plink_command()
+
+ geno_file_path = webqtlConfig.GENODIR+self.name+".geno"
+ plink_file_path = PLINK_PATH+"/"+self.name+".fam"
+
+ if os.path.isfile(plink_file_path):
+ self.samplelist = get_group_samplelists.get_samplelist("plink", plink_file_path)
+ elif os.path.isfile(geno_file_path):
+ self.samplelist = get_group_samplelists.get_samplelist("geno", geno_file_path)
+ else:
self.samplelist = None
print("after get_samplelist")
Redis.set(key, json.dumps(self.samplelist))
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index 48d8cd0a..330fec56 100755
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -53,7 +53,7 @@ GNROOT = "/home/zas1024/gene/" # Will remove this and dependent items later
SECUREDIR = GNROOT + 'secure/'
COMMON_LIB = GNROOT + 'support/admin'
HTMLPATH = GNROOT + 'genotype_files/'
-PYLMM_PATH = '/home/zas1024/plink/'
+PYLMM_PATH = '/home/zas1024/plink_gemma/'
SNP_PATH = '/home/zas1024/snps/'
IMGDIR = GNROOT + '/wqflask/wqflask/images/'
IMAGESPATH = HTMLPATH + 'images/'