From 3fbb71e93d63f405555d10f9caa10709675dcbdf Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Thu, 24 Mar 2022 11:30:39 +0100
Subject: [PATCH] Allow custom info columns in counts table.
---
libcodonusage/libcodonusage.py | 14 ++++++++------
1 file changed, 8 insertions(+), 6 deletions(-)
diff --git a/libcodonusage/libcodonusage.py b/libcodonusage/libcodonusage.py
index 7721658..5167856 100644
--- a/libcodonusage/libcodonusage.py
+++ b/libcodonusage/libcodonusage.py
@@ -280,16 +280,18 @@ might be excluded.
def make_counts_only(
counts_table,
- seq_id_kw="locus_tag", alt_tag_kw="old_locus_tag"):
+ seq_id_kw="locus_tag", alt_tag_kw="old_locus_tag",
+ ref_info_cols=None):
"""
Integrate "informative" columns of *counts_table* into the index.
"""
# To ensure a stable order:
- ref_info_cols = [
- alt_tag_kw, seq_id_kw,
- "start", "end", "length",
- "start_codon", "expected_start_aa",
- "first_stop", "nb_stops", "start_upstream", "end_downstream"]
+ if ref_info_cols is None:
+ ref_info_cols = [
+ alt_tag_kw, seq_id_kw,
+ "start", "end", "length",
+ "start_codon", "expected_start_aa",
+ "first_stop", "nb_stops", "start_upstream", "end_downstream"]
# To ensure no info columns are lost:
info_cols = [
counts_table.index.name,
--
GitLab