diff options
| -rwxr-xr-x | wqflask/base/data_set.py | 15 | ||||
| -rw-r--r-- | wqflask/wqflask/correlation/show_corr_results.py | 65 |
2 files changed, 67 insertions, 13 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 5d21c901..16f9da5d 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -1078,7 +1078,20 @@ class MrnaAssayDataSet(DataSet): def retrieve_gene_symbols(self): query = """ - select ProbeSet.Name, ProbeSet.Symbol + 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; diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 42d5acd6..5df2f316 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -133,7 +133,7 @@ class CorrelationResults(object): if self.corr_type == "tissue": trait_symbol_dict = self.dataset.retrieve_gene_symbols() - tissue_corr_data = self.do_tissue_corr_for_all_traits(trait_gene_symbols = trait_symbol_dict) + tissue_corr_data = self.do_tissue_correlation_for_all_traits(trait_gene_symbols = trait_symbol_dict) #print("tissue_corr_data: ", pf(tissue_corr_data)) for trait in tissue_corr_data.keys()[:self.return_number]: @@ -158,8 +158,12 @@ class CorrelationResults(object): #self.correlation_data[trait] = [sample_r, sample_p, num_overlap] elif self.corr_type == "lit": - trait_symbol_dict = self.dataset.retrieve_gene_symbols() + trait_geneid_dict = self.dataset.retrieve_gene_ids() + lit_corr_data = self.do_lit_correlation_for_all_traits(trait_gene_ids = trait_geneid_dict) + for trait in lit_corr_data.keys()[:self.return_number]: + self.get_sample_r_and_p_values(trait = trait, target_samples = self.target_dataset.trait_data[trait]) + elif self.corr_type == "sample": for trait, values in self.target_dataset.trait_data.iteritems(): self.get_sample_r_and_p_values(trait = trait, target_samples = values) @@ -181,13 +185,15 @@ class CorrelationResults(object): #Get symbol for trait and call function that gets each tissue value from the database (tables TissueProbeSetXRef, #TissueProbeSetData, etc) and calculates the correlation (cal_zero_order_corr_for_tissue in correlation_functions) + # Set some sane defaults + trait_object.tissue_corr = 0 + trait_object.tissue_pvalue = 0 + trait_object.lit_corr = 0 if self.corr_type == "tissue": trait_object.tissue_corr = tissue_corr_data[trait][1] trait_object.tissue_pvalue = tissue_corr_data[trait][2] - else: - # Set some sane defaults - trait_object.tissue_corr = 0 - trait_object.tissue_pvalue = 0 + elif self.corr_type == "lit": + trait_object.lit_corr = lit_corr_data[trait][1] self.correlation_results.append(trait_object) @@ -299,7 +305,7 @@ class CorrelationResults(object): #return self.correlation_results - def do_tissue_corr_for_all_traits(self, trait_gene_symbols, tissue_dataset_id=1): + def do_tissue_correlation_for_all_traits(self, trait_gene_symbols, tissue_dataset_id=1): #Gets tissue expression values for the primary trait primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values( symbol_list = [self.this_trait.symbol]) @@ -336,7 +342,7 @@ class CorrelationResults(object): def do_lit_correlation_for_trait_list(self): input_trait_mouse_gene_id = self.convert_to_mouse_gene_id(self.dataset.group.species.lower(), self.this_trait.geneid) - + for trait in self.correlation_results: if trait.geneid: @@ -350,7 +356,7 @@ class CorrelationResults(object): FROM LCorrRamin3 WHERE GeneId1='%s' and GeneId2='%s' - """ % (escape(trait.mouse_gene_id), escape(self.this_trait.geneid)) + """ % (escape(trait.mouse_gene_id), escape(input_trait_mouse_gene_id)) ).fetchone() if not result: result = g.db.execute("""SELECT value @@ -361,9 +367,7 @@ class CorrelationResults(object): ).fetchone() if result: - lit_corr = result.value - - if lit_corr: + lit_corr = result.value trait.lit_corr = lit_corr else: trait.lit_corr = 0 @@ -371,6 +375,43 @@ class CorrelationResults(object): trait.lit_corr = 0 + def do_lit_correlation_for_all_traits(self, trait_gene_ids): + input_trait_mouse_gene_id = self.convert_to_mouse_gene_id(self.dataset.group.species.lower(), self.this_trait.geneid) + + lit_corr_data = {} + for trait, gene_id in trait_gene_ids.iteritems(): + mouse_gene_id = self.convert_to_mouse_gene_id(self.dataset.group.species.lower(), gene_id) + + if mouse_gene_id and str(mouse_gene_id).find(";") == -1: + print("gene_symbols:", input_trait_mouse_gene_id + " / " + mouse_gene_id) + result = g.db.execute( + """SELECT value + FROM LCorrRamin3 + WHERE GeneId1='%s' and + GeneId2='%s' + """ % (escape(mouse_gene_id), escape(input_trait_mouse_gene_id)) + ).fetchone() + if not result: + result = g.db.execute("""SELECT value + FROM LCorrRamin3 + WHERE GeneId2='%s' and + GeneId1='%s' + """ % (escape(mouse_gene_id), escape(input_trait_mouse_gene_id)) + ).fetchone() + if result: + print("result:", result) + lit_corr = result.value + lit_corr_data[trait] = [gene_id, lit_corr] + else: + lit_corr_data[trait] = [gene_id, 0] + else: + lit_corr_data[trait] = [gene_id, 0] + + lit_corr_data = collections.OrderedDict(sorted(lit_corr_data.items(), + key=lambda t: -abs(t[1][1]))) + + return lit_corr_data + def convert_to_mouse_gene_id(self, species=None, gene_id=None): """If the species is rat or human, translate the gene_id to the mouse geneid |