Add SGE script

Script3_results_analysis.py

@@ -47,7 +47,7 @@ data = pd.read_csv(results_file, sep = '\t')
 
 # All significant associations (one line per Phenotype - SNP association)
 results_snps = significant_snps(data, pheno_list, res_list, th)
-#results_snps = add_genes_ucsc(results_snps, summary_directory) # Use UCSC database to match SNPs with genes
+results_snps = add_genes_ucsc(results_snps, summary_directory) # Use UCSC database to match SNPs with genes
 results_snps.to_csv(summary_snps_file, sep = '\t', index = 0)
 
 # Associations grouped by region, i.e. independent LD blocks (one line per Phenotype - Region association)

others/Script3_functions.py

@@ -134,6 +134,7 @@ def significant_snps(df, pheno_list, res_list, th):
 #     *chromEnd = End position in chromosome
 #################################################################################################################################
 def add_genes_ucsc(results_snps, summary_directory):
+    
     tmp_file = summary_directory + '/tmp_ucsc'
     
     list_snps = np.unique(results_snps['SNP']) # list of significant snps