diff --git a/libcodonusage/__init__.py b/libcodonusage/__init__.py index 3c99cc9f3ccb64a7561ba49140c0d1ce353fba55..c45672d8a14f37072d6d1dd6f5f7b99fc9b464f4 100644 --- a/libcodonusage/__init__.py +++ b/libcodonusage/__init__.py @@ -1,6 +1,6 @@ __copyright__ = "Copyright (C) 2022 Blaise Li" __licence__ = "GNU GPLv3" -__version__ = "0.21" +__version__ = "0.22" from .libcodonusage import ( aa2colour, aa_usage, diff --git a/libcodonusage/libcodonusage.py b/libcodonusage/libcodonusage.py index 94d722f40a86189a3541412d0175918388eb1000..8b136fc0d3586466c7954634030c20da221b0af2 100644 --- a/libcodonusage/libcodonusage.py +++ b/libcodonusage/libcodonusage.py @@ -352,7 +352,7 @@ SUZUKI_DOI = "10.1016/j.febslet.2005.10.032" SUZUKI_LINK = f"[Suzuki et al (2005)](https://doi.org/{SUZUKI_DOI})" -def gene_wide_codon_usage(codon_counts, verbose=False): +def gene_wide_codon_usage(codon_counts, verbose=False, return_props=False): """ Compute codon usage biases "gene-wide" as the standardized difference between a gene's codon proportions and global @@ -414,10 +414,12 @@ across genes) so that they are more comparable between codons. # standardized_codon_usage_biases.style.hide(axis="index") if verbose: display(standardized_codon_usage_biases.head(3)) + if return_props: + return (standardized_codon_usage_biases, codon_proportions) return standardized_codon_usage_biases -def by_aa_codon_usage(codon_counts, verbose=False): +def by_aa_codon_usage(codon_counts, verbose=False, return_props=False): """ Compute codon usage biases "by amino-acid" as the standardized difference between a gene's codon proportions and global @@ -495,10 +497,12 @@ across genes) so that they are more comparable between codons. # standardized_codon_usage_biases.style.hide(axis="index") if verbose: display(standardized_codon_usage_biases.head(3)) + if return_props: + return (standardized_codon_usage_biases, codon_proportions) return standardized_codon_usage_biases -def aa_usage(codon_counts, verbose=False): +def aa_usage(codon_counts, verbose=False, return_props=False): """ Compute amino-acid usage biases as the standardized difference between a gene's amino-acid proportions @@ -563,6 +567,8 @@ across genes) so that they are more comparable between amino-acids. # standardized_aa_usage_biases.style.hide(axis="index") if verbose: display(standardized_aa_usage_biases.head(3)) + if return_props: + return (standardized_aa_usage_biases, aa_proportions) return standardized_aa_usage_biases @@ -1319,7 +1325,7 @@ def violin_usage_by_clusters_splitby( for clss in classes: fig = violin_usage_by_clusters( usage_with_clusters.loc[ - (*(slice(None) for _ in range(idx_level)), clss),], + (*(slice(None) for _ in range(idx_level)), clss), ], aa, ylabel_template + f" for {clss}", cluster_level_template=cluster_level_template, vertical=vertical, **violin_kwargs)