def run(self):
folder = os.path.split(self.output_file)[0]
if len(folder) and not os.path.exists(folder):
os.makedirs(folder)
if os.path.exists(self.output_file):
logging.info("Results path %s already exists, delete it if you want it to be calculated again", self.output_file)
return
logging.info("Loading people")
people_by_id = None
if os.path.exists(self.selected_dosage_folder):
samples_path = Utilities.samplesInputPath(self.selected_dosage_folder)
if samples_path is not None:
people = Person.Person.loadPeople(samples_path)
people_by_id = {p.id:p for p in people}
logging.info("Loading weights from database: %s" % (self.weight_db_path))
weight_db_logic = WeightDBUtilities.WeightDBEntryLogic(self.weight_db_path)
results = None
normalization = None
results, normalization = self.resultsFromCovarianceFile(weight_db_logic)
self.saveEntries(self.output_file, results, normalization)
def run(self):
folder = os.path.split(self.output_file)[0]
if len(folder) and not os.path.exists(folder):
os.makedirs(folder)
if os.path.exists(self.output_file):
logging.info(
"Results path %s already exists, delete it if you want it to be calculated again",
self.output_file)
return
people_by_id = None
if os.path.exists(self.selected_dosage_folder):
logging.info("Loading people")
samples_path = Utilities.samplesInputPath(
self.selected_dosage_folder)
if samples_path is not None:
people = Person.Person.loadPeople(samples_path)
people_by_id = {p.id: p for p in people}
logging.info("Loading weights from database: %s" %
(self.weight_db_path))
weight_db_logic = WeightDBUtilities.WeightDBEntryLogic(
self.weight_db_path)
#Normalization is ignored at the moment. Not sure if it will return.
results = None
normalization = None
results, normalization = self.resultsFromCovarianceFile(
weight_db_logic)
self.saveEntries(self.output_file, results)
logging.info("Successfully ran MetaXcan analysis")
def __init__(self, args):
self.dosage_folder = args.dosage_folder
self.snp_list = args.snp_list
self.output_folder = args.output_folder
self.input_format = args.input_format
self.output_format = args.output_format
self.population_group_filters = args.population_group_filters
self.individual_filters = [re.compile(x) for x in args.individual_filters]
self.chromosome_in_name_regex = re.compile(args.file_pattern)
self.samples_input = Utilities.samplesInputPath(self.dosage_folder)
samples_name = os.path.split(self.samples_input)[1]
self.samples_output = os.path.join(self.output_folder, samples_name)
def __init__(self, args):
self.dosage_folder = args.dosage_folder
self.snp_list = args.snp_list
self.output_folder = args.output_folder
self.input_format = args.input_format
self.output_format = args.output_format
self.population_group_filters = args.population_group_filters
self.individual_filters = [
re.compile(x) for x in args.individual_filters
]
self.chromosome_in_name_regex = re.compile(args.file_pattern)
self.samples_input = Utilities.samplesInputPath(self.dosage_folder)
samples_name = os.path.split(self.samples_input)[1]
self.samples_output = os.path.join(self.output_folder, samples_name)
def testSamplesInputPath(self):
path = Utilities.samplesInputPath("tests/_td/dosage_set_1")
self.assertEqual(path, "tests/_td/dosage_set_1/set.sample")
def testSamplesInputPath(self):
path = Utilities.samplesInputPath("tests/_td/dosage_set_1")
self.assertEqual(path, "tests/_td/dosage_set_1/set.sample")
