diff options
Diffstat (limited to 'wqflask/base/data_set.py')
| -rwxr-xr-x | wqflask/base/data_set.py | 29 |
1 files changed, 10 insertions, 19 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 0e5a3ac1..c6f34143 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -44,12 +44,15 @@ from dbFunction import webqtlDatabaseFunction from utility import webqtlUtil from utility.benchmark import Bench from utility import chunks +from utility.tools import flat_files 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 = {} @@ -404,15 +407,11 @@ class DatasetGroup(object): else: #print("Cache not hit") - from utility.tools import plink_command - PLINK_RUN = plink_command() - geno_file_path = webqtlConfig.GENODIR+self.name+".geno" - plink_file_path = PLINK_PATH+"/"+self.name+".fam" - # @FIXME PJOTR/ZACH: .fam files should go into FLATFILES - if os.path.isfile(plink_file_path): - self.samplelist = get_group_samplelists.get_samplelist("plink", plink_file_path) + mapping_file_path = MAPPING_PATH+"/"+self.name+".fam" + 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) else: @@ -441,18 +440,10 @@ class DatasetGroup(object): # 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 os.path.isfile(full_filename): - #print("Reading file: ", full_filename) - genotype_1.read(full_filename) - #print("File read") - else: - try: - full_filename = str(os.path.join(webqtlConfig.TMPDIR, self.name + '.geno')) - #print("Reading file") - genotype_1.read(full_filename) - #print("File read") - except IOError: - print("File doesn't exist!") + if not os.path.isfile(full_filename): + raise SystemError("File "+full_filename+" does not exist") + print("Reading file: ", full_filename) + genotype_1.read(full_filename) if genotype_1.type == "group" and self.parlist: genotype_2 = genotype_1.add(Mat=self.parlist[0], Pat=self.parlist[1]) #, F1=_f1) |