diff options
Diffstat (limited to 'wqflask/base/data_set.py')
| -rwxr-xr-x | wqflask/base/data_set.py | 161 |
1 files changed, 143 insertions, 18 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 111597a9..1520b180 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -23,6 +23,8 @@ from __future__ import absolute_import, print_function, division import os import math +import string +import collections import json import itertools @@ -49,23 +51,29 @@ def create_dataset(dataset_name): query = """ SELECT DBType.Name FROM DBList, DBType - WHERE DBList.Name = '%s' and + WHERE DBList.Name = '{}' and DBType.Id = DBList.DBTypeId - """ % (escape(dataset_name)) - print("query is: ", pf(query)) + """.format(escape(dataset_name)) + #print("query is: ", pf(query)) dataset_type = g.db.execute(query).fetchone().Name #dataset_type = cursor.fetchone()[0] - print("[blubber] dataset_type:", pf(dataset_type)) + #print("[blubber] dataset_type:", pf(dataset_type)) dataset_ob = DS_NAME_MAP[dataset_type] #dataset_class = getattr(data_set, dataset_ob) - print("dataset_ob:", dataset_ob) - print("DS_NAME_MAP:", pf(DS_NAME_MAP)) + #print("dataset_ob:", dataset_ob) + #print("DS_NAME_MAP:", pf(DS_NAME_MAP)) dataset_class = globals()[dataset_ob] return dataset_class(dataset_name) +def mescape(*items): + """Multiple escape""" + escaped = [escape(item) for item in items] + print("escaped is:", escaped) + return escaped + class Markers(object): """Todo: Build in cacheing so it saves us reading the same file more than once""" @@ -74,15 +82,21 @@ class Markers(object): self.markers = json.load(json_data_fh) def add_pvalues(self, p_values): + print("length of self.markers:", len(self.markers)) + print("length of p_values:", len(p_values)) + # THIS IS only needed for the case when we are limiting the number of p-values calculated - if len(self.markers) > len(p_values): + 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): 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 + + class HumanMarkers(Markers): @@ -93,9 +107,9 @@ class HumanMarkers(Markers): for line in marker_data_fh: splat = line.strip().split() marker = {} - marker['chr'] = splat[0] + marker['chr'] = int(splat[0]) marker['name'] = splat[1] - marker['Mb'] = str(float(splat[3]) / 1000000) + marker['Mb'] = float(splat[3]) / 1000000 self.markers.append(marker) #print("markers is: ", pf(self.markers)) @@ -116,8 +130,7 @@ class HumanMarkers(Markers): with Bench("deleting markers"): markers = [] for marker in self.markers: - #if not float(marker['Mb']) <= 0 or not float(marker['chr']) == 0: - if float(marker['Mb']) > 0 and marker['chr'] != "0": + if not marker['Mb'] <= 0 and not marker['chr'] == 0: markers.append(marker) self.markers = markers @@ -349,6 +362,19 @@ class PhenotypeDataSet(DataSet): # (Urgently?) Need to write this pass + def get_trait_list(self): + query = """ + select PublishXRef.Id + from PublishXRef, PublishFreeze + where PublishFreeze.InbredSetId=PublishXRef.InbredSetId + and PublishFreeze.Id = {} + """.format(escape(str(self.id))) + results = g.db.execute(query).fetchall() + trait_data = {} + for trait in results: + trait_data[trait[0]] = self.retrieve_sample_data(trait[0]) + return trait_data + def get_trait_info(self, trait_list, species = ''): for this_trait in trait_list: if not this_trait.haveinfo: @@ -359,9 +385,7 @@ class PhenotypeDataSet(DataSet): 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 - this_trait.description_display = description.decode('utf-8') - - + this_trait.description_display = description if not this_trait.year.isdigit(): this_trait.pubmed_text = "N/A" @@ -419,7 +443,7 @@ class PhenotypeDataSet(DataSet): PublishFreeze.Id = %d AND PublishData.StrainId = Strain.Id Order BY Strain.Name - """ % (trait.name, self.id) + """ % (trait, self.id) results = g.db.execute(query).fetchall() return results @@ -459,6 +483,19 @@ class GenotypeDataSet(DataSet): def check_confidentiality(self): return geno_mrna_confidentiality(self) + + def get_trait_list(self): + query = """ + select Geno.Name + from Geno, GenoXRef + where GenoXRef.GenoId = Geno.Id + and GenoFreezeId = {} + """.format(escape(str(self.id))) + results = g.db.execute(query).fetchall() + trait_data = {} + for trait in results: + trait_data[trait[0]] = self.retrieve_sample_data(trait[0]) + return trait_data def get_trait_info(self, trait_list, species=None): for this_trait in trait_list: @@ -497,7 +534,7 @@ class GenotypeDataSet(DataSet): GenoData.StrainId = Strain.Id Order BY Strain.Name - """ % (webqtlDatabaseFunction.retrieve_species_id(self.group.name), trait.name, self.name) + """ % (webqtlDatabaseFunction.retrieve_species_id(self.group.name), trait, self.name) results = g.db.execute(query).fetchall() return results @@ -569,7 +606,95 @@ class MrnaAssayDataSet(DataSet): def check_confidentiality(self): return geno_mrna_confidentiality(self) + + def get_trait_list_1(self): + query = """ + select ProbeSet.Name + from ProbeSet, ProbeSetXRef + where ProbeSetXRef.ProbeSetId = ProbeSet.Id + 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): + sample_ids = [] + for sample in self.group.samplelist: + query = """ + SELECT Strain.Id FROM Strain, Species + WHERE Strain.Name = '{}' + and Strain.SpeciesId=Species.Id + and Species.name = '{}' + """.format(*mescape(sample, self.group.species)) + this_id = g.db.execute(query).fetchone()[0] + sample_ids.append('%d' % this_id) + print("sample_ids size: ", len(sample_ids)) + + # MySQL limits the number of tables that can be used in a join to 61, + # so we break the sample ids into smaller chunks + chunk_count = 50 + n = len(sample_ids) / chunk_count + if len(sample_ids) % chunk_count: + n += 1 + print("n: ", n) + #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) + trait_sample_data = [] + for step in range(int(n)): + temp = [] + sample_ids_step = sample_ids[step*chunk_count:min(len(sample_ids), (step+1)*chunk_count)] + for item in sample_ids_step: + temp.append('T%s.value' % item) + 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)) + #XZ, 03/04/2009: Xiaodong changed Data to %sData and changed parameters from %(item,item, db.type,item,item) to %(db.type, item,item, db.type,item,item) + 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)) + print("query: ", query) + 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 j in range(trait_count): + trait_name = trait_sample_data[0][j][0] + for i in range(int(n)): + self.trait_data[trait_name] += trait_sample_data[i][j][data_start_pos:] + def get_trait_info(self, trait_list=None, species=''): # Note: setting trait_list to [] is probably not a great idea. @@ -693,9 +818,9 @@ class MrnaAssayDataSet(DataSet): ProbeSetFreeze.Name = %s """ % (escape(self.name), escape(self.dataset.name)) results = g.db.execute(query).fetchone() - return results[0] + def retrieve_sample_data(self, trait): query = """ SELECT @@ -712,7 +837,7 @@ class MrnaAssayDataSet(DataSet): ProbeSetData.StrainId = Strain.Id Order BY Strain.Name - """ % (escape(trait.name), escape(self.name)) + """ % (escape(trait), escape(self.name)) results = g.db.execute(query).fetchall() return results |