diff options
| -rwxr-xr-x | wqflask/base/data_set.py | 16 |
1 files changed, 5 insertions, 11 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index c6f34143..9ffc09ac 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -44,15 +44,13 @@ from dbFunction import webqtlDatabaseFunction from utility import webqtlUtil from utility.benchmark import Bench from utility import chunks -from utility.tools import flat_files +from utility.tools import locate from maintenance import get_group_samplelists from MySQLdb import escape_string as escape from pprint import pformat as pf -MAPPING_PATH = flat_files("mapping") - # Used by create_database to instantiate objects # Each subclass will add to this DS_NAME_MAP = {} @@ -405,11 +403,10 @@ class DatasetGroup(object): #print(" type: ", type(self.samplelist)) #print(" self.samplelist: ", self.samplelist) else: - #print("Cache not hit") - - geno_file_path = webqtlConfig.GENODIR+self.name+".geno" + print("Cache not hit") - mapping_file_path = MAPPING_PATH+"/"+self.name+".fam" + geno_file_path = locate(self.name+".geno",'genotype') + mapping_file_path = locate(self.name+".fam",'mapping') if os.path.isfile(mapping_file_path): self.samplelist = get_group_samplelists.get_samplelist("plink", mapping_file_path) elif os.path.isfile(geno_file_path): @@ -439,10 +436,7 @@ class DatasetGroup(object): genotype_1 = reaper.Dataset() # reaper barfs on unicode filenames, so here we ensure it's a string - full_filename = str(os.path.join(webqtlConfig.GENODIR, self.name + '.geno')) - if not os.path.isfile(full_filename): - raise SystemError("File "+full_filename+" does not exist") - print("Reading file: ", full_filename) + full_filename = str(locate(self.name+'.geno','genotype')) genotype_1.read(full_filename) if genotype_1.type == "group" and self.parlist: |