From 10fdccc3f9879405000ce36c504194d8a9848f90 Mon Sep 17 00:00:00 2001
From: hjulienn <hanna.julienne@pasteur.fr>
Date: Mon, 18 Sep 2023 13:15:31 +0200
Subject: [PATCH] remove duplicated index in imputed SNPs
---
raiss/windows.py | 12 +++++++++---
1 file changed, 9 insertions(+), 3 deletions(-)
diff --git a/raiss/windows.py b/raiss/windows.py
index e583bb4..8452055 100644
--- a/raiss/windows.py
+++ b/raiss/windows.py
@@ -32,8 +32,15 @@ def realigned_zfiles_on_panel(ref_panel, zscore):
- ref_panel (pd.dataframe) : snp of reference on the imputed chromosome
- zscore (pd.dataframe):
"""
- zscore.drop_duplicates(keep='first', inplace=True)
- ref_panel.drop_duplicates(keep='first', inplace=True)
+
+ # Remove SNPs with duplicated index
+ print("Duplicated SNPs to be removed")
+ print(ref_panel[ref_panel.index.duplicated(keep='first')])
+ print(zscore[zscore.index.duplicated(keep='first')])
+
+ zscore = zscore[~zscore.index.duplicated(keep='first')]
+ ref_panel = ref_panel[~ref_panel.index.duplicated(keep='first')]
+
inter_id = zscore.index.intersection(ref_panel.index).drop_duplicates(keep='first')
zscore = zscore.loc[inter_id]
@@ -41,7 +48,6 @@ def realigned_zfiles_on_panel(ref_panel, zscore):
zscore.sort_index(inplace=True)
sub_ref_panel.sort_index(inplace=True)
-
allele_inverted = (sub_ref_panel.Ref_all != zscore.A0)
zscore.loc[allele_inverted, "A0"] = sub_ref_panel.loc[allele_inverted].Ref_all
--
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