From fd935ad8e5b9e43aab97e0e4dbeb43bd137b35ac Mon Sep 17 00:00:00 2001
From: Hanna JULIENNE <hanna.julienne@pasteur.fr>
Date: Mon, 19 Jul 2021 09:41:16 +0000
Subject: [PATCH] Update save_output.py
---
jass_preprocessing/save_output.py | 29 ++++++++++++++++-------------
1 file changed, 16 insertions(+), 13 deletions(-)
diff --git a/jass_preprocessing/save_output.py b/jass_preprocessing/save_output.py
index c66dc90..1379859 100644
--- a/jass_preprocessing/save_output.py
+++ b/jass_preprocessing/save_output.py
@@ -12,19 +12,22 @@ def save_output_by_chromosome(mgwas, ImpG_output_Folder, my_study):
mgwas_copy.dropna(subset=["computed_z"], how="any", inplace=True)
print(mgwas_copy.index.unique())
for chrom in mgwas_copy.index.unique():
- print(mgwas_copy.loc[chrom])
- mgwas_chr = pd.DataFrame({
- 'rsID': mgwas_copy.loc[chrom].snp_id,
- 'pos': mgwas_copy.loc[chrom].pos,
- 'A0': mgwas_copy.loc[chrom].ref,
- 'A1':mgwas_copy.loc[chrom].alt,
- 'Z': mgwas_copy.loc[chrom].computed_z,
- 'P': mgwas_copy.loc[chrom].pval
- }, columns= ['rsID', 'pos', 'A0', "A1", "Z", "P" ])
-
- impg_output_file = ImpG_output_Folder + 'z_'+ my_study +'_chr'+str(chrom)+".txt"
- print("WRITING CHR {} results for {} to: {}".format(chrom, my_study, ImpG_output_Folder))
- mgwas_chr.sort_values(by="pos").to_csv(impg_output_file, sep="\t", index=False)
+ if type(mgwas_copy.loc[chrom]) is pd.core.frame.DataFrame:
+ print(mgwas_copy.loc[chrom])
+ mgwas_chr = pd.DataFrame({
+ 'rsID': mgwas_copy.loc[chrom].snp_id,
+ 'pos': mgwas_copy.loc[chrom].pos,
+ 'A0': mgwas_copy.loc[chrom].ref,
+ 'A1':mgwas_copy.loc[chrom].alt,
+ 'Z': mgwas_copy.loc[chrom].computed_z,
+ 'P': mgwas_copy.loc[chrom].pval
+ }, columns= ['rsID', 'pos', 'A0', "A1", "Z", "P" ])
+
+ impg_output_file = ImpG_output_Folder + 'z_'+ my_study +'_chr'+str(chrom)+".txt"
+ print("WRITING CHR {} results for {} to: {}".format(chrom, my_study, ImpG_output_Folder))
+ mgwas_chr.sort_values(by="pos").to_csv(impg_output_file, sep="\t", index=False)
+ else:
+ print("NO or 1 value for CHR {} results for {} to: {}".format(chrom, my_study, ImpG_output_Folder))
def save_output(mgwas, ImpG_output_Folder, my_study):
--
GitLab