diff options
| -rwxr-xr-x | wqflask/base/data_set.py | 17 | ||||
| -rw-r--r-- | wqflask/wqflask/correlation/show_corr_results.py | 19 |
2 files changed, 16 insertions, 20 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 20c9a24f..beb62bd7 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -436,8 +436,13 @@ class DataSet(object): print("Dataset {} is not yet available in GeneNetwork.".format(self.name)) pass - def get_trait_data(self): - self.samplelist = self.group.samplelist + self.group.parlist + self.group.f1list + def get_trait_data(self, sample_list=None): + if sample_list: + self.samplelist = sample_list + self.group.parlist + self.group.f1list + else: + self.samplelist = self.group.samplelist + self.group.parlist + self.group.f1list + + query = """ SELECT Strain.Name, Strain.Id FROM Strain, Species WHERE Strain.Name IN {} @@ -1085,16 +1090,8 @@ class MrnaAssayDataSet(DataSet): ProbeSetXRef.ProbeSetId=ProbeSet.Id; """ % (column_name, escape(str(self.id))) results = g.db.execute(query).fetchall() - print("in retrieve_genes results {}: {}".format(type(results), results)) return dict(results) - - #return {item[0]: item[1] for item in results} - - #symbol_dict = {} - #for item in results: - # symbol_dict[item[0]] = item[1] - #return symbol_dict #def retrieve_gene_symbols(self): # query = """ diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 258dcfa4..a5c80674 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -70,7 +70,7 @@ TISSUE_MOUSE_DB = 1 def print_mem(stage=""): mem = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss - print("{}: {}".format(stage, mem/1024)) + #print("{}: {}".format(stage, mem/1024)) class AuthException(Exception): @@ -119,10 +119,14 @@ class CorrelationResults(object): #exclude the primary samples (because they would have been added in the previous #if statement if the user selected All Samples) if corr_samples_group != 'samples_primary': + if corr_samples_group == 'samples_other': + primary_samples = [x for x in primary_samples if x not in ( + self.dataset.group.parlist + self.dataset.group.f1list)] + print("primary_samples:", primary_samples) self.process_samples(start_vars, self.this_trait.data.keys(), primary_samples) self.target_dataset = data_set.create_dataset(start_vars['corr_dataset']) - self.target_dataset.get_trait_data() + self.target_dataset.get_trait_data(self.sample_data.keys()) self.correlation_results = [] @@ -180,7 +184,7 @@ class CorrelationResults(object): if self.corr_type != "tissue": self.do_tissue_correlation_for_trait_list() - print("self.correlation_results: ", pf(self.correlation_results)) + #print("self.correlation_results: ", pf(self.correlation_results)) #XZ, 09/18/2008: get all information about the user selected database. @@ -241,8 +245,6 @@ class CorrelationResults(object): #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]) - - print("primary_trait_tissue_vals: ", pf(primary_trait_tissue_vals_dict)) if self.this_trait.symbol.lower() in primary_trait_tissue_vals_dict: primary_trait_tissue_values = primary_trait_tissue_vals_dict[self.this_trait.symbol.lower()] @@ -258,8 +260,6 @@ class CorrelationResults(object): corr_result_tissue_vals_dict= correlation_functions.get_trait_symbol_and_tissue_values( symbol_list=gene_symbol_list) - print("corr_result_tissue_vals: ", pf(corr_result_tissue_vals_dict)) - for trait in self.correlation_results: if trait.symbol and trait.symbol.lower() in corr_result_tissue_vals_dict: this_trait_tissue_values = corr_result_tissue_vals_dict[trait.symbol.lower()] @@ -430,14 +430,14 @@ class CorrelationResults(object): """ + print("len(self.sample_data):", len(self.sample_data)) + this_trait_vals = [] target_vals = [] for index, sample in enumerate(self.target_dataset.samplelist): if sample in self.sample_data: sample_value = self.sample_data[sample] - print("sample_value:", sample_value) target_sample_value = target_samples[index] - print("target_sample_value:", target_sample_value) this_trait_vals.append(sample_value) target_vals.append(target_sample_value) @@ -995,7 +995,6 @@ class CorrelationResults(object): values_2.append(target_value) correlation = calCorrelation(values_1, values_2) self.correlation_data[trait] = correlation - print ('correlation result: %s %s' % (trait, correlation)) """ correlations = [] |