From 6a80855825d65989e804c1beb4e337880d01f632 Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Wed, 2 Mar 2022 18:24:31 +0100
Subject: [PATCH] Counts table reformatting.
---
libcodonusage/__init__.py | 5 ++++-
libcodonusage/libcodonusage.py | 21 +++++++++++++++++++++
2 files changed, 25 insertions(+), 1 deletion(-)
diff --git a/libcodonusage/__init__.py b/libcodonusage/__init__.py
index 3eed697..12d8398 100644
--- a/libcodonusage/__init__.py
+++ b/libcodonusage/__init__.py
@@ -1,12 +1,15 @@
__copyright__ = "Copyright (C) 2022 Blaise Li"
__licence__ = "GNU GPLv3"
-__version__ = 0.3
+__version__ = 0.4
from .libcodonusage import (
aa2colour,
+ codon2aa,
columns_by_aa,
detect_fishy_genes,
load_bias_table,
load_counts_table,
+ make_aa_codon_columns,
+ make_counts_only,
render_md,
violin_usage,
violin_usage_vertical,
diff --git a/libcodonusage/libcodonusage.py b/libcodonusage/libcodonusage.py
index c577e32..b8ee559 100644
--- a/libcodonusage/libcodonusage.py
+++ b/libcodonusage/libcodonusage.py
@@ -224,6 +224,27 @@ def detect_fishy_genes(codon_counts):
return criteria
+def make_counts_only(counts_table):
+ """
+ Integrate "informative" columns of *counts_table* into the index.
+ """
+ info_cols = [
+ counts_table.index.name,
+ *counts_table.columns.difference(codon2aa)]
+ assert set(info_cols) == {
+ "old_locus_tag", "locus_tag", "length", "start_codon", "expected_start_aa",
+ "first_stop", "nb_stops", "start_upstream", "end_downstream"}
+ return counts_table.reset_index().set_index(info_cols)
+
+
+def make_aa_codon_columns(counts_table):
+ """Transform column headers into a (aa, codon) MultiIndex."""
+ counts_table.columns = pd.MultiIndex.from_tuples(
+ ((codon2aa[codon], codon) for codon in counts_table.columns),
+ names=("aa", "codon"))
+ return counts_table
+
+
def load_bias_table(table_path, nb_cluster_series=2):
"""
Load a table containing by-amino-acid codon usage biases.
--
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