From 28b03b1e317e9a73d0be04c8f6b526009cc9ab08 Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Wed, 8 Nov 2023 16:34:01 +0100
Subject: [PATCH] Change default output of group_codons_by_class.
The codons belonging to the classes are not present in the output.
---
libcodonusage/__init__.py | 2 +-
libcodonusage/libcodonusage.py | 34 ++++++++++++++++++----------------
2 files changed, 19 insertions(+), 17 deletions(-)
diff --git a/libcodonusage/__init__.py b/libcodonusage/__init__.py
index dc6f97f..998abc6 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__ = "0.28.5"
+__version__ = "0.29.0"
from .libcodonusage import (
aa2colour,
aa_usage,
diff --git a/libcodonusage/libcodonusage.py b/libcodonusage/libcodonusage.py
index 69aca04..856af0e 100644
--- a/libcodonusage/libcodonusage.py
+++ b/libcodonusage/libcodonusage.py
@@ -14,7 +14,7 @@
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
"""Functions used in Jupyter notebooks."""
-from itertools import combinations
+from itertools import chain, combinations
import json
from operator import attrgetter, itemgetter
from pathlib import Path
@@ -442,19 +442,13 @@ SUZUKI_DOI = "10.1016/j.febslet.2005.10.032"
SUZUKI_LINK = f"[Suzuki et al (2005)](https://doi.org/{SUZUKI_DOI})"
-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).
- """
- codon_counts.drop(columns=codon_list, inplace=True)
- 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).
+ When the columns of *codon_counts* are a MultiIndex with a first
+ level corresponding to the amino-acid and the second to the codon,
+ the codons should be specified as (aa, codon) tuples.
"""
return codon_counts.drop(columns=codon_list)
@@ -486,14 +480,14 @@ def max_codon_counts(row, codons):
def group_codons_by_class(
- codon_counts, group_name, dict_classes,
- mode="max", keep_only_groups=False):
+ codon_counts, group_name, codon_classes,
+ mode="max", keep_only_groups=False, replace_groups=True):
"""
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
+ *codon_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. It should be the name of
a method of the `GroupBy` object, like "sum" or "max".
@@ -502,14 +496,18 @@ def group_codons_by_class(
If *mode* is "sum", 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.
+ other codons than the ones specified in codon_classes.
If set to False (default), the original codon_counts table
is returned with additional columns for the grouped_classes.
+ If the boolean *replace_groups* is set to True (default), the full
+ count table will be returned, except the columns used to compute the
+ grouped values. This option is ignored if *keep_only_groups* has been
+ set to True.
"""
col_renames = {
(aa, codon): (class_name, group_name, codon)
- for class_name in dict_classes
- for (aa, codon) in dict_classes[class_name]}
+ for class_name in codon_classes
+ for (aa, codon) in codon_classes[class_name]}
codon_counts_pre_group = codon_counts[col_renames.keys()]
# We add a level to the column names,
# "codon", becoming "sub_codon", will disappear
@@ -524,6 +522,10 @@ def group_codons_by_class(
mode)()
if keep_only_groups:
return codon_counts_grouped
+ if replace_groups:
+ return remove_codons(
+ pd.concat([codon_counts, codon_counts_grouped], axis=1),
+ chain.from_iterable(codon_classes.values()))
return pd.concat([codon_counts, codon_counts_grouped], axis=1)
--
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