save log in csv

raiss/sanity_log.py

@@ -77,9 +77,22 @@ def report_snps(res_dict, trait, filename="raiss_report"):
         f.write(res_dict['R2_quality'].to_string())
     f.close()
 
+def report_snps_csv(res_dict, trait, filename="raiss_report"):
+    # I save the log in three .csv files.
+    df = pd.DataFrame({'Number of SNPs in harmonized file': [res_dict["total_harmonized"]],
+                       'Number of SNPs in imputed file': [res_dict["total_imputed"]],
+                       'Proportion imputed': [res_dict['proportion']]})
+    df.to_csv("{}_{}_Number_of_SNPs.csv".format(filename, trait), index=False)
+
+    # Number of SNPs by level of significance
+    res_dict['signif_count'].to_csv("{}_{}_Number_of_SNPs_by_level_of_significance.csv".format(filename, trait))
+
+    # Number of imputed SNPs by level of imputation quality
+    res_dict['R2_quality'].to_csv = "{}_{}_Number_of_SNPs_by_level_of_imputation_quality.csv".format(filename, trait)
+
 def raiss_report(trait, harmonized_folder, imputed_folder, filename="raiss_report", chr_list=range(1,23)):
     """
     Function to compute a report for one trait
     """
     res_dict = count_snps(trait, harmonized_folder, imputed_folder, chr_list)
-    report_snps(res_dict, trait, filename)
+    report_snps_csv(res_dict, trait, filename)