From de4b5e81f07418274fd1efd1745dc31bde119a88 Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Wed, 8 Nov 2023 15:41:39 +0100
Subject: [PATCH] Remove side effect of remove_codons.
---
libcodonusage/__init__.py | 2 +-
libcodonusage/libcodonusage.py | 50 ++++++----------------------------
2 files changed, 10 insertions(+), 42 deletions(-)
diff --git a/libcodonusage/__init__.py b/libcodonusage/__init__.py
index 81a2d1f..dc6f97f 100644
--- a/libcodonusage/__init__.py
+++ b/libcodonusage/__init__.py
@@ -1,6 +1,6 @@
__copyright__ = "Copyright (C) 2022-2023 Blaise Li, Marie Anselmet"
__licence__ = "GNU GPLv3"
-__version__ = "0.28.4"
+__version__ = "0.28.5"
from .libcodonusage import (
aa2colour,
aa_usage,
diff --git a/libcodonusage/libcodonusage.py b/libcodonusage/libcodonusage.py
index a1d4894..69aca04 100644
--- a/libcodonusage/libcodonusage.py
+++ b/libcodonusage/libcodonusage.py
@@ -442,7 +442,7 @@ SUZUKI_DOI = "10.1016/j.febslet.2005.10.032"
SUZUKI_LINK = f"[Suzuki et al (2005)](https://doi.org/{SUZUKI_DOI})"
-def remove_codons(codon_counts, codon_list):
+def remove_codons_old(codon_counts, codon_list):
"""
Filter out codons in a table *codon_counts* based on codons
present in the list *codon_list* (like stop codons).
@@ -451,6 +451,14 @@ def remove_codons(codon_counts, codon_list):
return codon_counts
+def remove_codons(codon_counts, codon_list):
+ """
+ Filter out codons in a table *codon_counts* based on codons
+ present in the list *codon_list* (like stop codons).
+ """
+ return codon_counts.drop(columns=codon_list)
+
+
def sum_codon_counts(row, codons):
"""
Perform the row-wise sum of codon counts for the codons
@@ -477,46 +485,6 @@ def max_codon_counts(row, codons):
return max(counts_codons)
-def group_codons_by_class_old(
- codon_counts, group_name, dict_classes,
- mode="max", keep_only_groups=False):
- """
- Group codons given specific classes in *codon_counts* table.
-
- *group_name* contains the name of the grouping, and plays the role
- of aa names in the original codon counts table.
- *dict_classes* contains the different classes under this grouping
- as keys and the associated list of codons as values.
- *mode* defines the way grouping is computed.
- If mode is "max", the maximum value of counts of codons belonging
- to the same class is used for the grouped class.
- Otherwise, the sum of counts values for all codons belonging to
- the same class is used for the grouped class.
- *keep_only_groups* is a boolean set to True if you want to filter out
- other codons than the ones specified in dict_classes.
- If set to False (default), the original codon_counts table
- is returned with additional columns for the grouped_classes.
- """
- list_classes_names = []
- # pylint issues the following warning:
- # "W0640: Cell variable value defined in loop (cell-var-from-loop)"
- # Since the lambda function is used immediately,
- # this should not be an actual issue
- # (see https://stackoverflow.com/q/25314547/1878788 and answers)
- for key, value in dict_classes.items():
- if mode == "max":
- codon_counts[group_name, key] = codon_counts.apply(
- lambda row: max_codon_counts(row, value), axis=1)
- else:
- codon_counts[group_name, key] = codon_counts.apply(
- lambda row: sum_codon_counts(row, value), axis=1)
- list_classes_names.append(key)
- if keep_only_groups:
- return codon_counts.loc[:, ([group_name], list_classes_names)]
- else:
- return codon_counts
-
-
def group_codons_by_class(
codon_counts, group_name, dict_classes,
mode="max", keep_only_groups=False):
--
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