From d2a976c99670946e7b297b2fbd5c52315f13efe6 Mon Sep 17 00:00:00 2001
From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr>
Date: Thu, 5 Mar 2020 16:52:18 +0100
Subject: [PATCH] src/db_utils/fill_exon_n_gene_table.py: fix
get_genomic_region function
---
src/db_utils/fill_exon_n_gene_table.py | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/src/db_utils/fill_exon_n_gene_table.py b/src/db_utils/fill_exon_n_gene_table.py
index d8d0fb87..3add88d7 100755
--- a/src/db_utils/fill_exon_n_gene_table.py
+++ b/src/db_utils/fill_exon_n_gene_table.py
@@ -21,8 +21,9 @@ def get_genomic_region(bed_file: Path) -> pd.DataFrame:
:param bed_file: A bed file containing intern exons
:return: the bed file as a dataframe
"""
- df = pd.read_csv(bed_file, sep="\t")
- df.columns = ["chromosome", "start", "stop", "id", "score", "strand"]
+ df = pd.read_csv(bed_file, sep="\t",
+ names=["chromosome", "start", "stop", "id",
+ "score", "strand"])
df = df.loc[(df.stop - df.start > 2), :]
return df
--
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