From 2a8b92187e2d93e818119de56e82f241d3385ef9 Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Fri, 6 Oct 2023 17:09:27 +0200
Subject: [PATCH] Added global R4 computation.
---
libcodonusage/__init__.py | 2 +-
libcodonusage/libcodonusage.py | 9 ++++++++-
2 files changed, 9 insertions(+), 2 deletions(-)
diff --git a/libcodonusage/__init__.py b/libcodonusage/__init__.py
index e82dd57..b1e7b77 100644
--- a/libcodonusage/__init__.py
+++ b/libcodonusage/__init__.py
@@ -1,6 +1,6 @@
__copyright__ = "Copyright (C) 2022-2023 Blaise Li"
__licence__ = "GNU GPLv3"
-__version__ = "0.28.0"
+__version__ = "0.28.1"
from .libcodonusage import (
aa2colour,
aa_usage,
diff --git a/libcodonusage/libcodonusage.py b/libcodonusage/libcodonusage.py
index f63e15b..bf629e2 100644
--- a/libcodonusage/libcodonusage.py
+++ b/libcodonusage/libcodonusage.py
@@ -667,6 +667,12 @@ We compute the global usage, as the sum of the counts for a given codon,
across genes.
""")
global_usage = counts_for_global.sum(axis=0)
+ if return_more:
+ # Same computation as for individual genes,
+ # but based on the total counts.
+ global_max_counts = global_usage.T.groupby("aa").max().T
+ global_r4 = global_usage.div(
+ global_max_counts)
render_md("Then we sum over codons corresponding to the same amino-acid.")
global_summed_by_aa = global_usage.groupby(level=0).sum()
render_md("""
@@ -702,7 +708,8 @@ across genes) so that they are more comparable between codons.
"rscu": rscu,
"r4_table": r4_table,
"global_proportions": global_proportions,
- "global_rscu": global_proportions.mul(degeneracy)}
+ "global_rscu": global_proportions.mul(degeneracy),
+ "global_r4": global_r4}
return standardized_codon_usage_biases
--
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