1.5.7

Release date: 2026-03-16

What's New

Selenocysteine support (fixes #420, #710)

hgvs can now correctly translate variants in selenocysteine-encoding transcripts. Selenocysteine (Sec) is a non-standard amino acid encoded by the UGA codon, which is normally a stop codon. Previously, variants in these transcripts would be incorrectly translated, the UGA codon would be interpreted as a stop, producing wrong protein-level HGVS representations.

What changed:

• c_to_p and g_to_p mappings now automatically detect selenocysteine transcripts by checking the reference protein sequence. No code changes are required by users.
• Selenocysteine is correctly represented as Sec in three-letter notation or U in single-letter notation.

Example:
NM_020451.3:c.380_382del → NP_065184.2:p.(Sec127del)
NC_000001.11:g.25812789T>C → NP_065184.2:p.(Sec462Arg)

Upgrade Notes

This release is a drop-in replacement for 1.5.6. No API changes are required. If you were previously working around incorrect translations for selenocysteine transcripts (e.g., GPX family genes), those workarounds can now be removed.

Full Changelog: 1.5.6...1.5.7

1.5.6

A series of minor improvements that we are releasing before merging in some major changes into the main branch.

Includes fix #774 Deletions including the stop codon should be frameshifts

1.5.5

Bug Fixes

• Ensure hgvs seqrepo dir is unset during testing by @ccaitlingo in #669
• #652 - Fix for Error: AttributeError: 'UTA_postgresql' object has no attribute '_pool' by @davmlaw in #666
• Fix typo in formatted string by @ecalifornica in #680
• #670 - Gene Symbol support dash and underscore by @davmlaw in #683
• Fix for issue 704 - pass on prevalidation_level by @davmlaw in #746
• fix: projection issue for stop retained insertion (#707) by @holtgrewe in #708
• fix(cicd): add cache-apt-pkgs-action to install zsh by @korikuzma in #754
• fix(test): add vcr_config for cassette management and re-run cassettes by @korikuzma in #755
• Fix exception in g_to_c mapping by @b0d0nne11 in #765
• Fix variant region for ins and dup on intron-exon boundary by @b0d0nne11 in #748
• fix(#712): This fixes the broken make develop install by @andreasprlic in #713
• #730 - Fix single letter amino acid bug by @jPleyte in #731
• #722 Babelfish VCF bugs by @davmlaw in #723

New Features

• #447 - implement babelfish for VCF by @davmlaw in #660
• #661 - Improve Parser startup time by storing generated Python code by @davmlaw in #664
• feat: update default data version config by @jsstevenson in #734
• feat(#741): Pretty print by @andreasprlic in #742
• Add variant region condition for dups ending in UTR by @b0d0nne11 in #716
• #744 - babelfish vcf conversion accept contig accessions as chrom names by @davmlaw in #745

Other Changes

• Updated instructions for hgvs readme by @ccaitlingo in #656

Internal and Developer Changes

• Remove unused variables by @ecalifornica in #681
• Remove unused string format argument by @ecalifornica in #678
• Remove superfluous import by @ecalifornica in #677
• Add inline ignore for line too long errors by @ecalifornica in #674
• Remove unused imports by @ecalifornica in #675
• Add isort profile configuration to match black by @ecalifornica in #672
• Fix undefined names by @ecalifornica in #679
• Fix linter complaint about ambiguous variable name by @ecalifornica in #676
• Explicitly define test imports by @ecalifornica in #686
• Remove unused variables by @ecalifornica in #685
• #689 - undo circular import introduced from linting fix by @davmlaw in #690
• Remove top level code environment script by @ecalifornica in #696
• updates to documentation by @katiestahl in #694
• Remove unused imports by @ecalifornica in #684
• Remove test HTTP network calls by @ecalifornica in #697
• #688 - remove future usage by @davmlaw in #726
• #695 - Remove top level code environment scripts from modules by @davmlaw in #728
• #178 - use abc for Edit class to ensure method definition by @davmlaw in #729
• chore: remove trailing whitespace by @jsstevenson in #737
• refactor: use importlib instead of pkg_resources by @jsstevenson in #738
• build: require python >= 3.10 by @jsstevenson in #739
• Update authors for 2024 (last updated 4 years ago) by @davmlaw in #752
• Remove python2 legacy by @davmlaw in #753
• Update test cache by @reece in #756
• Resolve testing warnings by @reece in #763
• update project config to pyproject.toml and drop krufty config by @reece in #769
• fix typo. Sentence about g -> r stated g -> c by @brechtmann in #772

New Contributors

• @ccaitlingo made their first contribution in #656
• @ecalifornica made their first contribution in #681
• @davmlaw made their first contribution in #660
• @katiestahl made their first contribution in #694
• @jPleyte made their first contribution in #731
• @jsstevenson made their first contribution in #734
• @b0d0nne11 made their first contribution in #716
• @holtgrewe made their first contribution in #708
• @brechtmann made their first contribution in #772

Full Changelog: 1.5.4...1.5.5