diff options
Diffstat (limited to 'wqflask/base/data_set.py')
| -rw-r--r-- | wqflask/base/data_set.py | 35 |
1 files changed, 21 insertions, 14 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 54dd3c4b..7f08135f 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -61,14 +61,17 @@ logger = getLogger(__name__ ) # Each subclass will add to this DS_NAME_MAP = {} -def create_dataset(dataset_name, dataset_type = None, get_samplelist = True): +def create_dataset(dataset_name, dataset_type = None, get_samplelist = True, group_name = None): if not dataset_type: dataset_type = Dataset_Getter(dataset_name) logger.debug("dataset_type", dataset_type) dataset_ob = DS_NAME_MAP[dataset_type] dataset_class = globals()[dataset_ob] - return dataset_class(dataset_name, get_samplelist) + if dataset_type == "Temp": + return dataset_class(dataset_name, get_samplelist, group_name) + else: + return dataset_class(dataset_name, get_samplelist) class Dataset_Types(object): @@ -261,10 +264,13 @@ class DatasetGroup(object): has multiple datasets associated with it. """ - def __init__(self, dataset): + def __init__(self, dataset, name=None): """This sets self.group and self.group_id""" #logger.debug("DATASET NAME2:", dataset.name) - self.name, self.id, self.genetic_type = fetchone(dataset.query_for_group) + if name == None: + self.name, self.id, self.genetic_type = fetchone(dataset.query_for_group) + else: + self.name, self.id, self.genetic_type = fetchone("SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType FROM InbredSet where Name='%s'" % name) if self.name == 'BXD300': self.name = "BXD" @@ -304,7 +310,7 @@ class DatasetGroup(object): elif mapping_id == "2": mapping_names = ["GEMMA"] elif mapping_id == "4": - mapping_names = ["PLINK"] + mapping_names = ["GEMMA", "PLINK"] else: mapping_names = [] @@ -319,9 +325,7 @@ class DatasetGroup(object): def check_plink_gemma(): if flat_file_exists("mapping"): MAPPING_PATH = flat_files("mapping")+"/" - if (os.path.isfile(MAPPING_PATH+self.name+".bed") and - (os.path.isfile(MAPPING_PATH+self.name+".map") or - os.path.isfile(MAPPING_PATH+self.name+".bim"))): + if os.path.isfile(MAPPING_PATH+self.name+".bed"): return True return False @@ -481,7 +485,7 @@ class DataSet(object): """ - def __init__(self, name, get_samplelist = True): + def __init__(self, name, get_samplelist = True, group_name = None): assert name, "Need a name" self.name = name @@ -493,11 +497,12 @@ class DataSet(object): self.setup() - self.check_confidentiality() - - self.retrieve_other_names() - - self.group = DatasetGroup(self) # sets self.group and self.group_id and gets genotype + if self.type == "Temp": #Need to supply group name as input if temp trait + self.group = DatasetGroup(self, group_name) # sets self.group and self.group_id and gets genotype + else: + self.check_confidentiality() + self.retrieve_other_names() + self.group = DatasetGroup(self) # sets self.group and self.group_id and gets genotype if get_samplelist == True: self.group.get_samplelist() self.species = species.TheSpecies(self) @@ -1156,6 +1161,8 @@ class MrnaAssayDataSet(DataSet): class TempDataSet(DataSet): '''Temporary user-generated data set''' + DS_NAME_MAP['Temp'] = 'TempDataSet' + def setup(self): self.search_fields = ['name', 'description'] |