diff options
Diffstat (limited to 'wqflask')
| -rwxr-xr-x | wqflask/base/data_set.py | 16 | ||||
| -rw-r--r-- | wqflask/utility/tools.py | 4 |
2 files changed, 11 insertions, 9 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 9ffc09ac..ce13dd77 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -44,7 +44,7 @@ from dbFunction import webqtlDatabaseFunction from utility import webqtlUtil from utility.benchmark import Bench from utility import chunks -from utility.tools import locate +from utility.tools import locate, locate_without_error from maintenance import get_group_samplelists @@ -405,15 +405,15 @@ class DatasetGroup(object): else: print("Cache not hit") - 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): - self.samplelist = get_group_samplelists.get_samplelist("geno", geno_file_path) + genotype_fn = locate_without_error(self.name+".geno",'genotype') + mapping_fn = locate_without_error(self.name+".fam",'mapping') + if mapping_fn: + self.samplelist = get_group_samplelists.get_samplelist("plink", mapping_fn) + elif genotype_fn: + self.samplelist = get_group_samplelists.get_samplelist("geno", genotype_fn) else: self.samplelist = None - #print("after get_samplelist") + print("Sample list: ",self.samplelist) Redis.set(key, json.dumps(self.samplelist)) Redis.expire(key, 60*5) diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index dd40be99..d4c10c68 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -36,7 +36,7 @@ def get_setting(command_id,guess=None): """ def value(command): if command: - sys.stderr.write("Found value "+command+"\n") + sys.stderr.write("Found path "+command+"\n") return command else: return None @@ -95,6 +95,7 @@ def locate(name, subdir=None): if valid_path(base): lookfor = base + "/" + name if valid_file(lookfor): + print("Found: file "+lookfor+"\n") return lookfor else: raise IOError("Can not locate "+lookfor) @@ -114,6 +115,7 @@ def locate_without_error(name, subdir=None): if valid_path(base): lookfor = base + "/" + name if valid_file(lookfor): + print("Found: file "+name+"\n") return lookfor sys.stderr.write("WARNING: file "+name+" not found\n") return None |