From ad2d5a2e8adace417c3b9ea6ff1f9f728c492e12 Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Thu, 14 Apr 2022 12:27:08 +0200
Subject: [PATCH] Option to return proportions too, not just biases.
---
libcodonusage/__init__.py | 2 +-
libcodonusage/libcodonusage.py | 14 ++++++++++----
2 files changed, 11 insertions(+), 5 deletions(-)
diff --git a/libcodonusage/__init__.py b/libcodonusage/__init__.py
index 3c99cc9..c45672d 100644
--- a/libcodonusage/__init__.py
+++ b/libcodonusage/__init__.py
@@ -1,6 +1,6 @@
__copyright__ = "Copyright (C) 2022 Blaise Li"
__licence__ = "GNU GPLv3"
-__version__ = "0.21"
+__version__ = "0.22"
from .libcodonusage import (
aa2colour,
aa_usage,
diff --git a/libcodonusage/libcodonusage.py b/libcodonusage/libcodonusage.py
index 94d722f..8b136fc 100644
--- a/libcodonusage/libcodonusage.py
+++ b/libcodonusage/libcodonusage.py
@@ -352,7 +352,7 @@ SUZUKI_DOI = "10.1016/j.febslet.2005.10.032"
SUZUKI_LINK = f"[Suzuki et al (2005)](https://doi.org/{SUZUKI_DOI})"
-def gene_wide_codon_usage(codon_counts, verbose=False):
+def gene_wide_codon_usage(codon_counts, verbose=False, return_props=False):
"""
Compute codon usage biases "gene-wide" as the standardized
difference between a gene's codon proportions and global
@@ -414,10 +414,12 @@ across genes) so that they are more comparable between codons.
# standardized_codon_usage_biases.style.hide(axis="index")
if verbose:
display(standardized_codon_usage_biases.head(3))
+ if return_props:
+ return (standardized_codon_usage_biases, codon_proportions)
return standardized_codon_usage_biases
-def by_aa_codon_usage(codon_counts, verbose=False):
+def by_aa_codon_usage(codon_counts, verbose=False, return_props=False):
"""
Compute codon usage biases "by amino-acid" as the standardized
difference between a gene's codon proportions and global
@@ -495,10 +497,12 @@ across genes) so that they are more comparable between codons.
# standardized_codon_usage_biases.style.hide(axis="index")
if verbose:
display(standardized_codon_usage_biases.head(3))
+ if return_props:
+ return (standardized_codon_usage_biases, codon_proportions)
return standardized_codon_usage_biases
-def aa_usage(codon_counts, verbose=False):
+def aa_usage(codon_counts, verbose=False, return_props=False):
"""
Compute amino-acid usage biases as the standardized
difference between a gene's amino-acid proportions
@@ -563,6 +567,8 @@ across genes) so that they are more comparable between amino-acids.
# standardized_aa_usage_biases.style.hide(axis="index")
if verbose:
display(standardized_aa_usage_biases.head(3))
+ if return_props:
+ return (standardized_aa_usage_biases, aa_proportions)
return standardized_aa_usage_biases
@@ -1319,7 +1325,7 @@ def violin_usage_by_clusters_splitby(
for clss in classes:
fig = violin_usage_by_clusters(
usage_with_clusters.loc[
- (*(slice(None) for _ in range(idx_level)), clss),],
+ (*(slice(None) for _ in range(idx_level)), clss), ],
aa, ylabel_template + f" for {clss}",
cluster_level_template=cluster_level_template,
vertical=vertical, **violin_kwargs)
--
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