diff options
| -rwxr-xr-x | wqflask/base/data_set.py | 228 |
1 files changed, 0 insertions, 228 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 8b2a9f01..52ac95f0 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -58,25 +58,13 @@ DS_NAME_MAP = {} def create_dataset(dataset_name, dataset_type = None, get_samplelist = True): if not dataset_type: dataset_type = Dataset_Getter(dataset_name) - #dataset_type = get_dataset_type_from_json(dataset_name) print("dataset_type is:", dataset_type) - #query = """ - # SELECT DBType.Name - # FROM DBList, DBType - # WHERE DBList.Name = '{}' and - # DBType.Id = DBList.DBTypeId - # """.format(escape(dataset_name)) - #dataset_type = g.db.execute(query).fetchone().Name - dataset_ob = DS_NAME_MAP[dataset_type] dataset_class = globals()[dataset_ob] return dataset_class(dataset_name, get_samplelist) - -#def get_dataset_type_from_json(dataset_name): - class Dataset_Types(object): def __init__(self): @@ -90,8 +78,6 @@ class Dataset_Types(object): for group in data['datasets'][species]: for dataset_type in data['datasets'][species][group]: for dataset in data['datasets'][species][group][dataset_type]: - #print("dataset is:", dataset) - short_dataset_name = dataset[1] if dataset_type == "Phenotypes": new_type = "Publish" @@ -107,10 +93,6 @@ class Dataset_Types(object): # Do the intensive work at startup one time only Dataset_Getter = Dataset_Types() -# -#print("Running at startup:", get_dataset_type_from_json("HBTRC-MLPFC_0611")) - - def create_datasets_list(): key = "all_datasets" result = Redis.get(key) @@ -215,13 +197,6 @@ class Markers(object): #del self.markers[i] self.markers = filtered_markers - - #for i, marker in enumerate(self.markers): - # if not 'p_value' in marker: - # #print("self.markers[i]", self.markers[i]) - # del self.markers[i] - # #self.markers.remove(self.markers[i]) - class HumanMarkers(Markers): def __init__(self, name, specified_markers = []): @@ -249,26 +224,8 @@ class HumanMarkers(Markers): def add_pvalues(self, p_values): - #for marker, p_value in itertools.izip(self.markers, p_values): - # if marker['Mb'] <= 0 and marker['chr'] == 0: - # continue - # marker['p_value'] = p_value - # print("p_value is:", marker['p_value']) - # marker['lod_score'] = -math.log10(marker['p_value']) - # #Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values - # marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61 - - #print("p_values2:", pf(p_values)) super(HumanMarkers, self).add_pvalues(p_values) - #with Bench("deleting markers"): - # markers = [] - # for marker in self.markers: - # if not marker['Mb'] <= 0 and not marker['chr'] == 0: - # markers.append(marker) - # self.markers = markers - - class DatasetGroup(object): """ @@ -311,12 +268,6 @@ class DatasetGroup(object): def datasets(self): key = "group_dataset_menu:v2:" + self.name print("key is2:", key) - #with Bench("Loading cache"): - # result = Redis.get(key) - #if result: - # self._datasets = pickle.loads(result) - # return self._datasets - dataset_menu = [] print("[tape4] webqtlConfig.PUBLICTHRESH:", webqtlConfig.PUBLICTHRESH) print("[tape4] type webqtlConfig.PUBLICTHRESH:", type(webqtlConfig.PUBLICTHRESH)) @@ -425,11 +376,6 @@ class DatasetGroup(object): def read_genotype_file(self): '''Read genotype from .geno file instead of database''' - #if self.group == 'BXD300': - # self.group = 'BXD' - # - #assert self.group, "self.group needs to be set" - #genotype_1 is Dataset Object without parents and f1 #genotype_2 is Dataset Object with parents and f1 (not for intercross) @@ -446,40 +392,16 @@ class DatasetGroup(object): #determine default genotype object if self.incparentsf1 and genotype_1.type != "intercross": - #self.genotype = genotype_2 genotype = genotype_2 else: self.incparentsf1 = 0 - #self.genotype = genotype_1 genotype = genotype_1 - #self.samplelist = list(self.genotype.prgy) self.samplelist = list(genotype.prgy) return genotype -#class DataSets(object): -# """Builds a list of DataSets""" -# -# def __init__(self): -# self.datasets = list() -# - - - #query = """SELECT Name FROM ProbeSetFreeze - # UNION - # SELECT Name From PublishFreeze - # UNION - # SELECT Name From GenoFreeze""" - # - #for result in g.db.execute(query).fetchall(): - # dataset = DataSet(result.Name) - # self.datasets.append(dataset) - -#ds = DataSets() -#print("[orange] ds:", ds.datasets) - class DataSet(object): """ DataSet class defines a dataset in webqtl, can be either Microarray, @@ -512,32 +434,11 @@ class DataSet(object): """Gets overridden later, at least for Temp...used by trait's get_given_name""" return None - #@staticmethod - #def get_by_trait_id(trait_id): - # """Gets the dataset object given the trait id""" - # - # - # - # name = g.db.execute(""" SELECT - # - # """) - # - # return DataSet(name) - # Delete this eventually @property def riset(): Weve_Renamed_This_As_Group - - #@property - #def group(self): - # if not self._group: - # self.get_group() - # - # return self._group - - def retrieve_other_names(self): """ If the data set name parameter is not found in the 'Name' field of the data set table, @@ -609,21 +510,6 @@ class DataSet(object): number_chunks = int(math.ceil(len(sample_ids) / chunk_size)) trait_sample_data = [] for sample_ids_step in chunks.divide_into_chunks(sample_ids, number_chunks): - - #XZ, 09/24/2008: build one temporary table that only contains the records associated with the input GeneId - #tempTable = None - #if GeneId and db.type == "ProbeSet": - # if method == "3": - # tempTable = self.getTempLiteratureTable(species=species, - # input_species_geneid=GeneId, - # returnNumber=returnNumber) - # - # if method == "4" or method == "5": - # tempTable = self.getTempTissueCorrTable(primaryTraitSymbol=GeneSymbol, - # TissueProbeSetFreezeId=tissueProbeSetFreezeId, - # method=method, - # returnNumber=returnNumber) - if self.type == "Publish": dataset_type = "Phenotype" else: @@ -1013,83 +899,11 @@ class MrnaAssayDataSet(DataSet): and ProbeSetFreezeId = {} """.format(escape(str(self.id))) results = g.db.execute(query).fetchall() - #print("After get_trait_list query") trait_data = {} for trait in results: - #print("Retrieving sample_data for ", trait[0]) trait_data[trait[0]] = self.retrieve_sample_data(trait[0]) - #print("After retrieve_sample_data") return trait_data - #def get_trait_data(self): - # self.samplelist = self.group.samplelist + self.group.parlist + self.group.f1list - # query = """ - # SELECT Strain.Name, Strain.Id FROM Strain, Species - # WHERE Strain.Name IN {} - # and Strain.SpeciesId=Species.Id - # and Species.name = '{}' - # """.format(create_in_clause(self.samplelist), *mescape(self.group.species)) - # results = dict(g.db.execute(query).fetchall()) - # sample_ids = [results[item] for item in self.samplelist] - # - # # MySQL limits the number of tables that can be used in a join to 61, - # # so we break the sample ids into smaller chunks - # # Postgres doesn't have that limit, so we can get rid of this after we transition - # chunk_size = 50 - # number_chunks = int(math.ceil(len(sample_ids) / chunk_size)) - # trait_sample_data = [] - # for sample_ids_step in chunks.divide_into_chunks(sample_ids, number_chunks): - # - # #XZ, 09/24/2008: build one temporary table that only contains the records associated with the input GeneId - # #tempTable = None - # #if GeneId and db.type == "ProbeSet": - # # if method == "3": - # # tempTable = self.getTempLiteratureTable(species=species, - # # input_species_geneid=GeneId, - # # returnNumber=returnNumber) - # # - # # if method == "4" or method == "5": - # # tempTable = self.getTempTissueCorrTable(primaryTraitSymbol=GeneSymbol, - # # TissueProbeSetFreezeId=tissueProbeSetFreezeId, - # # method=method, - # # returnNumber=returnNumber) - # - # temp = ['T%s.value' % item for item in sample_ids_step] - # query = "SELECT {}.Name,".format(escape(self.type)) - # data_start_pos = 1 - # query += string.join(temp, ', ') - # query += ' FROM ({}, {}XRef, {}Freeze) '.format(*mescape(self.type, - # self.type, - # self.type)) - # - # for item in sample_ids_step: - # query += """ - # left join {}Data as T{} on T{}.Id = {}XRef.DataId - # and T{}.StrainId={}\n - # """.format(*mescape(self.type, item, item, self.type, item, item)) - # - # query += """ - # WHERE {}XRef.{}FreezeId = {}Freeze.Id - # and {}Freeze.Name = '{}' - # and {}.Id = {}XRef.{}Id - # order by {}.Id - # """.format(*mescape(self.type, self.type, self.type, self.type, - # self.name, self.type, self.type, self.type, self.type)) - # results = g.db.execute(query).fetchall() - # trait_sample_data.append(results) - # - # trait_count = len(trait_sample_data[0]) - # self.trait_data = collections.defaultdict(list) - # - # # put all of the separate data together into a dictionary where the keys are - # # trait names and values are lists of sample values - # for trait_counter in range(trait_count): - # trait_name = trait_sample_data[0][trait_counter][0] - # for chunk_counter in range(int(number_chunks)): - # self.trait_data[trait_name] += ( - # trait_sample_data[chunk_counter][trait_counter][data_start_pos:]) - - def get_trait_info(self, trait_list=None, species=''): # Note: setting trait_list to [] is probably not a great idea. @@ -1178,22 +992,9 @@ class MrnaAssayDataSet(DataSet): result = g.db.execute(query).fetchone() if result: - #if result[0] and result[1]: - # lrs_chr = result[0] - # lrs_mb = result[1] lrs_chr, lrs_mb = result #XZ: LRS_location_value is used for sorting lrs_location_value = self.convert_location_to_value(lrs_chr, lrs_mb) - - #try: - # lrs_location_value = int(lrs_chr)*1000 + float(lrs_mb) - #except: - # if lrs_chr.upper() == 'X': - # lrs_location_value = 20*1000 + float(lrs_mb) - # else: - # lrs_location_value = (ord(str(LRS_chr).upper()[0])*1000 + - # float(lrs_mb)) - this_trait.LRS_score_repr = '%3.1f' % this_trait.lrs this_trait.LRS_score_value = this_trait.lrs this_trait.LRS_location_repr = 'Chr%s: %.6f' % (lrs_chr, float(lrs_mb)) @@ -1259,35 +1060,6 @@ class MrnaAssayDataSet(DataSet): return dict(results) - #def retrieve_gene_symbols(self): - # query = """ - # select ProbeSet.Name, ProbeSet.Symbol, ProbeSet.GeneId - # from ProbeSet,ProbeSetXRef - # where ProbeSetXRef.ProbeSetFreezeId = %s and - # ProbeSetXRef.ProbeSetId=ProbeSet.Id; - # """ % (self.id) - # results = g.db.execute(query).fetchall() - # symbol_dict = {} - # for item in results: - # symbol_dict[item[0]] = item[1] - # return symbol_dict - # - #def retrieve_gene_ids(self): - # query = """ - # select ProbeSet.Name, ProbeSet.GeneId - # from ProbeSet,ProbeSetXRef - # where ProbeSetXRef.ProbeSetFreezeId = %s and - # ProbeSetXRef.ProbeSetId=ProbeSet.Id; - # """ % (self.id) - # return process_and_run_query(query) - # results = g.db.execute(query).fetchall() - # symbol_dict = {} - # for item in results: - # symbol_dict[item[0]] = item[1] - # return symbol_dict - - - class TempDataSet(DataSet): '''Temporary user-generated data set''' |