diff options
Diffstat (limited to 'wqflask/base')
| -rwxr-xr-x | wqflask/base/data_set.py | 194 | ||||
| -rwxr-xr-x | wqflask/base/webqtlFormData.py | 2 |
2 files changed, 98 insertions, 98 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index ce13dd77..6527657a 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -76,22 +76,22 @@ def create_dataset(dataset_name, dataset_type = None, get_samplelist = True): #def get_dataset_type_from_json(dataset_name): - + class Dataset_Types(object): - + def __init__(self): self.datasets = {} file_name = "wqflask/static/new/javascript/dataset_menu_structure.json" with open(file_name, 'r') as fh: data = json.load(fh) - + print("*" * 70) for species in data['datasets']: 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" @@ -100,32 +100,32 @@ class Dataset_Types(object): else: new_type = "ProbeSet" self.datasets[short_dataset_name] = new_type - + def __call__(self, name): return self.datasets[name] - + # 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) - + if result: print("Cache hit!!!") datasets = pickle.loads(result) - + else: datasets = list() with Bench("Creating DataSets object"): type_dict = {'Publish': 'PublishFreeze', 'ProbeSet': 'ProbeSetFreeze', 'Geno': 'GenoFreeze'} - + for dataset_type in type_dict: query = "SELECT Name FROM {}".format(type_dict[dataset_type]) for result in g.db.execute(query).fetchall(): @@ -134,10 +134,10 @@ def create_datasets_list(): #print("type: {}\tname: {}".format(dataset_type, result.Name)) dataset = create_dataset(result.Name, dataset_type) datasets.append(dataset) - + Redis.set(key, pickle.dumps(datasets, pickle.HIGHEST_PROTOCOL)) Redis.expire(key, 60*60) - + return datasets @@ -158,30 +158,30 @@ def mescape(*items): class Markers(object): """Todo: Build in cacheing so it saves us reading the same file more than once""" def __init__(self, name): - json_data_fh = open(os.path.join(webqtlConfig.NEWGENODIR + name + '.json')) + json_data_fh = open(locate(name + '.json','genotype/json')) try: markers = json.load(json_data_fh) except: markers = [] - + for marker in markers: if (marker['chr'] != "X") and (marker['chr'] != "Y"): marker['chr'] = int(marker['chr']) marker['Mb'] = float(marker['Mb']) - + self.markers = markers #print("self.markers:", self.markers) - - + + def add_pvalues(self, p_values): print("length of self.markers:", len(self.markers)) print("length of p_values:", len(p_values)) - + if type(p_values) is list: # THIS IS only needed for the case when we are limiting the number of p-values calculated #if len(self.markers) > len(p_values): # self.markers = self.markers[:len(p_values)] - + for marker, p_value in itertools.izip(self.markers, p_values): if not p_value: continue @@ -214,7 +214,7 @@ class Markers(object): #self.markers.remove(marker) #del self.markers[i] self.markers = filtered_markers - + #for i, marker in enumerate(self.markers): # if not 'p_value' in marker: @@ -223,9 +223,9 @@ class Markers(object): # #self.markers.remove(self.markers[i]) class HumanMarkers(Markers): - + def __init__(self, name, specified_markers = []): - marker_data_fh = open(os.path.join(webqtlConfig.PYLMM_PATH + name + '.bim')) + marker_data_fh = open(locate('genotype') + '/' + name + '.bim') self.markers = [] for line in marker_data_fh: splat = line.strip().split() @@ -244,7 +244,7 @@ class HumanMarkers(Markers): marker['name'] = splat[1] marker['Mb'] = float(splat[3]) / 1000000 self.markers.append(marker) - + #print("markers is: ", pf(self.markers)) @@ -257,26 +257,26 @@ class HumanMarkers(Markers): # 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): """ Each group has multiple datasets; each species has multiple groups. - + For example, Mouse has multiple groups (BXD, BXA, etc), and each group has multiple datasets associated with it. - + """ def __init__(self, dataset): """This sets self.group and self.group_id""" @@ -284,14 +284,14 @@ class DatasetGroup(object): self.name, self.id = g.db.execute(dataset.query_for_group).fetchone() if self.name == 'BXD300': self.name = "BXD" - + self.f1list = None self.parlist = None self.get_f1_parent_strains() #print("parents/f1s: {}:{}".format(self.parlist, self.f1list)) - + self.species = webqtlDatabaseFunction.retrieve_species(self.name) - + self.incparentsf1 = False self.allsamples = None self._datasets = None @@ -302,7 +302,7 @@ class DatasetGroup(object): def get_markers(self): #print("self.species is:", self.species) if self.species == "human": - marker_class = HumanMarkers + marker_class = HumanMarkers else: marker_class = Markers @@ -356,7 +356,7 @@ class DatasetGroup(object): dataset_menu.append(dict(tissue=None, datasets=[(dataset, dataset_short)])) else: dataset_sub_menu = [item[1:] for item in dataset] - + tissue_already_exists = False tissue_position = None for i, tissue_dict in enumerate(dataset_menu): @@ -384,7 +384,7 @@ class DatasetGroup(object): f1, f12, maternal, paternal = webqtlUtil.ParInfo[self.name] except KeyError: f1 = f12 = maternal = paternal = None - + if f1 and f12: self.f1list = [f1, f12] if maternal and paternal: @@ -455,18 +455,18 @@ class DatasetGroup(object): #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 @@ -501,7 +501,7 @@ class DataSet(object): 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() @@ -511,30 +511,30 @@ class DataSet(object): def get_desc(self): """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 - # + # + # + # 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 @@ -546,7 +546,7 @@ class DataSet(object): This is not meant to retrieve the data set info if no name at all is passed. """ - + try: if self.type == "ProbeSet": query_args = tuple(escape(x) for x in ( @@ -582,17 +582,17 @@ class DataSet(object): except TypeError: print("Dataset {} is not yet available in GeneNetwork.".format(self.name)) pass - + def get_trait_data(self, sample_list=None): if sample_list: self.samplelist = sample_list else: self.samplelist = self.group.samplelist - + if self.group.parlist != None and self.group.f1list != None: if (self.group.parlist + self.group.f1list) in self.samplelist: self.samplelist += self.group.parlist + self.group.f1list - + query = """ SELECT Strain.Name, Strain.Id FROM Strain, Species WHERE Strain.Name IN {} @@ -610,9 +610,9 @@ class DataSet(object): 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 + #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 GeneId and db.type == "ProbeSet": # if method == "3": # tempTable = self.getTempLiteratureTable(species=species, # input_species_geneid=GeneId, @@ -623,7 +623,7 @@ class DataSet(object): # TissueProbeSetFreezeId=tissueProbeSetFreezeId, # method=method, # returnNumber=returnNumber) - + if self.type == "Publish": dataset_type = "Phenotype" else: @@ -644,7 +644,7 @@ class DataSet(object): left join {}Data as T{} on T{}.Id = {}XRef.DataId and T{}.StrainId={}\n """.format(*mescape(self.type, item, item, self.type, item, item)) - + if self.type == "Publish": query += """ WHERE {}XRef.InbredSetId = {}Freeze.InbredSetId @@ -661,16 +661,16 @@ class DataSet(object): order by {}.Id """.format(*mescape(self.type, self.type, self.type, self.type, self.name, dataset_type, self.type, self.type, dataset_type)) - + #print("trait data query: ", query) - + results = g.db.execute(query).fetchall() #print("query results:", results) 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): @@ -683,9 +683,9 @@ class PhenotypeDataSet(DataSet): DS_NAME_MAP['Publish'] = 'PhenotypeDataSet' def setup(self): - + #print("IS A PHENOTYPEDATASET") - + # Fields in the database table self.search_fields = ['Phenotype.Post_publication_description', 'Phenotype.Pre_publication_description', @@ -756,26 +756,26 @@ class PhenotypeDataSet(DataSet): def get_trait_info(self, trait_list, species = ''): for this_trait in trait_list: - + if not this_trait.haveinfo: this_trait.retrieve_info(get_qtl_info=True) description = this_trait.post_publication_description - + #If the dataset is confidential and the user has access to confidential #phenotype traits, then display the pre-publication description instead #of the post-publication description if this_trait.confidential: this_trait.description_display = "" continue # for now - + if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait( privilege=self.privilege, userName=self.userName, authorized_users=this_trait.authorized_users): - + description = this_trait.pre_publication_description - + if len(description) > 0: this_trait.description_display = description.strip() else: @@ -820,7 +820,7 @@ class PhenotypeDataSet(DataSet): this_trait.LRS_score_repr = LRS_score_repr = '%3.1f' % this_trait.lrs this_trait.LRS_score_value = LRS_score_value = this_trait.lrs this_trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (LRS_Chr, float(LRS_Mb)) - + def retrieve_sample_data(self, trait): query = """ SELECT @@ -878,7 +878,7 @@ class GenotypeDataSet(DataSet): def check_confidentiality(self): return geno_mrna_confidentiality(self) - + def get_trait_list(self): query = """ select Geno.Name @@ -912,7 +912,7 @@ class GenotypeDataSet(DataSet): this_trait.location_repr = 'Chr%s: %.6f' % (this_trait.chr, float(this_trait.mb) ) this_trait.location_value = trait_location_value - + def retrieve_sample_data(self, trait): query = """ SELECT @@ -1004,7 +1004,7 @@ class MrnaAssayDataSet(DataSet): def check_confidentiality(self): return geno_mrna_confidentiality(self) - + def get_trait_list_1(self): query = """ select ProbeSet.Name @@ -1020,7 +1020,7 @@ class MrnaAssayDataSet(DataSet): 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 = """ @@ -1040,9 +1040,9 @@ class MrnaAssayDataSet(DataSet): # 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 + # #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 GeneId and db.type == "ProbeSet": # # if method == "3": # # tempTable = self.getTempLiteratureTable(species=species, # # input_species_geneid=GeneId, @@ -1053,7 +1053,7 @@ class MrnaAssayDataSet(DataSet): # # 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 @@ -1067,7 +1067,7 @@ class MrnaAssayDataSet(DataSet): # 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 = '{}' @@ -1080,7 +1080,7 @@ class MrnaAssayDataSet(DataSet): # # 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): @@ -1088,11 +1088,11 @@ class MrnaAssayDataSet(DataSet): # 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. + # Note: setting trait_list to [] is probably not a great idea. if not trait_list: trait_list = [] @@ -1155,7 +1155,7 @@ class MrnaAssayDataSet(DataSet): #print("query is:", pf(query)) result = g.db.execute(query).fetchone() - + mean = result[0] if result else 0 if mean: @@ -1176,7 +1176,7 @@ class MrnaAssayDataSet(DataSet): Geno.SpeciesId = Species.Id """.format(species, this_trait.locus) result = g.db.execute(query).fetchone() - + if result: #if result[0] and result[1]: # lrs_chr = result[0] @@ -1184,7 +1184,7 @@ class MrnaAssayDataSet(DataSet): 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: @@ -1197,7 +1197,7 @@ class MrnaAssayDataSet(DataSet): 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)) - + def convert_location_to_value(self, chromosome, mb): try: @@ -1208,7 +1208,7 @@ class MrnaAssayDataSet(DataSet): else: location_value = (ord(str(chromosome).upper()[0])*1000 + float(mb)) - + return location_value def get_sequence(self): @@ -1225,7 +1225,7 @@ class MrnaAssayDataSet(DataSet): """ % (escape(self.name), escape(self.dataset.name)) results = g.db.execute(query).fetchone() return results[0] - + def retrieve_sample_data(self, trait): query = """ SELECT @@ -1246,8 +1246,8 @@ class MrnaAssayDataSet(DataSet): results = g.db.execute(query).fetchall() #print("RETRIEVED RESULTS HERE:", results) return results - - + + def retrieve_genes(self, column_name): query = """ select ProbeSet.Name, ProbeSet.%s @@ -1256,7 +1256,7 @@ class MrnaAssayDataSet(DataSet): ProbeSetXRef.ProbeSetId=ProbeSet.Id; """ % (column_name, escape(str(self.id))) results = g.db.execute(query).fetchall() - + return dict(results) #def retrieve_gene_symbols(self): @@ -1285,8 +1285,8 @@ class MrnaAssayDataSet(DataSet): # for item in results: # symbol_dict[item[0]] = item[1] # return symbol_dict - - + + class TempDataSet(DataSet): @@ -1308,8 +1308,8 @@ class TempDataSet(DataSet): self.id = 1 self.fullname = 'Temporary Storage' self.shortname = 'Temp' - - + + @staticmethod def handle_pca(desc): if 'PCA' in desc: @@ -1318,13 +1318,13 @@ class TempDataSet(DataSet): else: desc = desc[:desc.index('entered')].strip() return desc - + def get_desc(self): g.db.execute('SELECT description FROM Temp WHERE Name=%s', self.name) desc = g.db.fetchone()[0] desc = self.handle_pca(desc) - return desc - + return desc + def get_group(self): self.cursor.execute(""" SELECT @@ -1337,7 +1337,7 @@ class TempDataSet(DataSet): """, self.name) self.group, self.group_id = self.cursor.fetchone() #return self.group - + def retrieve_sample_data(self, trait): query = """ SELECT @@ -1351,7 +1351,7 @@ class TempDataSet(DataSet): Order BY Strain.Name """ % escape(trait.name) - + results = g.db.execute(query).fetchall() diff --git a/wqflask/base/webqtlFormData.py b/wqflask/base/webqtlFormData.py index 44fdcc3f..10251756 100755 --- a/wqflask/base/webqtlFormData.py +++ b/wqflask/base/webqtlFormData.py @@ -157,7 +157,7 @@ class webqtlFormData(object): self.genotype_1 = reaper.Dataset() - full_filename = os.path.join(webqtlConfig.GENODIR, self.group + '.geno') + full_filename = locate(self.group + '.geno','genotype') # reaper barfs on unicode filenames, so here we ensure it's a string full_filename = str(full_filename) |