diff options
Diffstat (limited to 'wqflask/base')
| -rwxr-xr-x | wqflask/base/data_set.py | 17 | ||||
| -rwxr-xr-x | wqflask/base/webqtlConfig.py | 2 |
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/' |