From 86c31e4f4b9a44ba7f3ab0fa2484d47035b7600e Mon Sep 17 00:00:00 2001
From: Hubble <hubble@HubbledeMacBook-Pro.local>
Date: Mon, 13 Nov 2023 00:08:39 +0100
Subject: [PATCH] save log in csv
---
raiss/sanity_log.py | 15 ++++++++++++++-
1 file changed, 14 insertions(+), 1 deletion(-)
diff --git a/raiss/sanity_log.py b/raiss/sanity_log.py
index 11df959..5e26181 100644
--- a/raiss/sanity_log.py
+++ b/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)
--
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