From 38e995ca47183e5d5d4f1dec7881984fb84d4d70 Mon Sep 17 00:00:00 2001 From: Samuele Soraggi Date: Tue, 24 Mar 2026 15:11:07 +0200 Subject: [PATCH] Change delimiter in CSV read from delim_whitespace to sep now deprecated in pandas --- pops.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pops.py b/pops.py index ae028a5..6149089 100644 --- a/pops.py +++ b/pops.py @@ -91,14 +91,14 @@ def get_indices_in_target_order(ref_list, target_names): ### --------------------------------- READING DATA --------------------------------- ### def read_gene_annot_df(gene_annot_path): - gene_annot_df = pd.read_csv(gene_annot_path, delim_whitespace=True).set_index("ENSGID") + gene_annot_df = pd.read_csv(gene_annot_path, sep='\s+').set_index("ENSGID") gene_annot_df["CHR"] = gene_annot_df["CHR"].astype(str) return gene_annot_df def read_magma(magma_prefix, use_magma_covariates, use_magma_error_cov): ### Get Y and Y_ids - magma_df = pd.read_csv(magma_prefix + ".genes.out", delim_whitespace=True) + magma_df = pd.read_csv(magma_prefix + ".genes.out", sep='\s+') Y = magma_df.ZSTAT.values Y_ids = magma_df.GENE.values if use_magma_covariates is not None or use_magma_error_cov is not None: