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")