From fa1283b6cc284d9290619d2e0eae86516a69f0ca Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Wed, 9 Mar 2022 15:08:39 +0100
Subject: [PATCH] Handle new input and border cases.
---
libcodonusage/__init__.py | 2 +-
libcodonusage/libcodonusage.py | 24 ++++++++++++++++++------
2 files changed, 19 insertions(+), 7 deletions(-)
diff --git a/libcodonusage/__init__.py b/libcodonusage/__init__.py
index cd647f6..33f7a90 100644
--- a/libcodonusage/__init__.py
+++ b/libcodonusage/__init__.py
@@ -1,6 +1,6 @@
__copyright__ = "Copyright (C) 2022 Blaise Li"
__licence__ = "GNU GPLv3"
-__version__ = 0.6
+__version__ = 0.7
from .libcodonusage import (
aa2colour,
codon2aa,
diff --git a/libcodonusage/libcodonusage.py b/libcodonusage/libcodonusage.py
index e8c8eea..fe0429c 100644
--- a/libcodonusage/libcodonusage.py
+++ b/libcodonusage/libcodonusage.py
@@ -86,7 +86,8 @@ with Path(bgraphs.colorschemes._scheme_dir).joinpath(
aa2colour = {**colscheme["colors"], "*": '#000000'}
-def load_counts_table(table_path, index_col="old_locus_tag"):
+def load_counts_table(
+ table_path, index_col="old_locus_tag", index_unique=True):
"""
Load a table or pre-computed codon counts at *table_path*.
@@ -94,9 +95,14 @@ def load_counts_table(table_path, index_col="old_locus_tag"):
Besides the columns containing the counts for each codon,
there are other columns containing various pieces of information
regarding those genes.
+
+ If *index_unique* is True, a ValueError error will be raised if
+ some elements in the the column *index_col* are not unique.
"""
render_md(f"Loading data from [{table_path}]({table_path})...\n")
codon_counts = pd.read_table(table_path, index_col=index_col)
+ if index_unique and not(codon_counts.index.is_unique):
+ raise ValueError(f"Index {index_col} contains repeated values.\n")
nb_genes = len(codon_counts)
render_md(
f"""
@@ -144,9 +150,12 @@ def compute_criteria(codon_counts):
display(criteria.agg(sum))
render_md("Upset plot of the non-empty categories:\n\n")
fig = plt.figure()
- UpSet(
- from_indicators(*[criteria.columns], data=criteria),
- show_counts=True).plot(fig=fig)
+ try:
+ UpSet(
+ from_indicators(*[criteria.columns], data=criteria),
+ show_counts=True).plot(fig=fig)
+ except AttributeError:
+ pass
display(fig)
plt.close(fig)
gene_sets = {
@@ -261,13 +270,16 @@ might be excluded.
return criteria
-def make_counts_only(counts_table):
+def make_counts_only(
+ counts_table,
+ seq_id_kw="locus_tag", alt_tag_kw="old_locus_tag"):
"""
Integrate "informative" columns of *counts_table* into the index.
"""
# To ensure a stable order:
ref_info_cols = [
- "old_locus_tag", "locus_tag", "length",
+ alt_tag_kw, seq_id_kw,
+ "start", "end", "length",
"start_codon", "expected_start_aa",
"first_stop", "nb_stops", "start_upstream", "end_downstream"]
# To ensure no info columns are lost:
--
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