From 3b410576d246121d22ee3266efffd132b1be47f4 Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Mon, 14 Mar 2022 17:42:32 +0100
Subject: [PATCH] Function to exclude columns with only NaNs.
---
libcodonusage/__init__.py | 3 ++-
libcodonusage/libcodonusage.py | 24 ++++++++++++++++++++++++
2 files changed, 26 insertions(+), 1 deletion(-)
diff --git a/libcodonusage/__init__.py b/libcodonusage/__init__.py
index 5b810c1..3107f30 100644
--- a/libcodonusage/__init__.py
+++ b/libcodonusage/__init__.py
@@ -1,6 +1,6 @@
__copyright__ = "Copyright (C) 2022 Blaise Li"
__licence__ = "GNU GPLv3"
-__version__ = "0.11"
+__version__ = "0.12"
from .libcodonusage import (
aa2colour,
aa_usage,
@@ -8,6 +8,7 @@ from .libcodonusage import (
codon2aa,
columns_by_aa,
detect_fishy_genes,
+ exclude_all_nan_cols,
gene_wide_codon_usage,
load_bias_table,
load_counts_table,
diff --git a/libcodonusage/libcodonusage.py b/libcodonusage/libcodonusage.py
index 761e24e..edc2ecd 100644
--- a/libcodonusage/libcodonusage.py
+++ b/libcodonusage/libcodonusage.py
@@ -545,6 +545,30 @@ across genes) so that they are more comparable between amino-acids.
return standardized_aa_usage_biases
+def exclude_all_nan_cols(standardized_usage_biases):
+ """
+ Detect columns in *standardized_usage_biases* that contain only NaNs
+ and remove them from the table.
+ """
+ render_md("""
+Standardization may result in division by zero for usage biases
+that have a zero standard deviation.
+This is expected to be the case for "by amino-acid" usage biases
+for codons corresponding to amino-acids having only one codon:
+methionine (M) and tryptophan (W).
+""")
+ all_nan_cols = standardized_usage_biases.columns[
+ standardized_usage_biases.isna().all()]
+ if len(all_nan_cols):
+ render_md("The following columns contain only NaNs:")
+ display(all_nan_cols)
+ render_md("This likely resulted from a division by zero.")
+ render_md("These columns will be excluded")
+ return (
+ standardized_usage_biases.drop(columns=all_nan_cols).fillna(0),
+ all_nan_cols)
+
+
def load_bias_table(table_path, nb_info_cols=9, nb_cluster_series=2):
"""
Load a table containing by-amino-acid codon usage biases.
--
GitLab