Module codon 

Codon translation, DNA complement, and VEP-style display formatting.

All functions operate on uppercase ASCII bytes (b'A', b'C', b'G', b'T'). The codon lookup tables use an internal 6-bit encoding but callers never see it — pass raw ASCII in, get ASCII out.

Genetic codes

Two translation tables are provided:

• Standard (NCBI table 1) — used for all autosomal and sex-chromosome transcripts. translate_codon uses this table.
• Vertebrate mitochondrial (NCBI table 2) — used for chrM transcripts. Four codons differ: TGA→W, AGA→*, AGG→*, ATA→M.

translate_codon_for_transcript dispatches to the correct table based on an is_mitochondrial flag (derived from transcript.chrom == "chrM").

Functions

aa_three_letter

Convert a one-letter amino acid code to its three-letter abbreviation.

complement

Complement a single DNA base. A↔T, C↔G. Non-ACGT bytes (e.g., N) pass through unchanged.

complement_in_place

Complement a DNA sequence in place. Each base is replaced with its Watson-Crick complement; non-ACGT bytes are left unchanged.

format_amino_acids

Format amino acid change for VEP display.

format_amino_acids_indel

Format amino acid change for indels.

format_codons

Format ref/alt codons with VEP’s capitalization convention.

format_codons_indel

Format ref/alt codon sequences for an indel with VEP’s capitalisation convention.

reverse_complement

Return the reverse complement of a DNA sequence.

translate_codon

Translate a 3-base codon to a single amino acid character using the standard genetic code (NCBI table 1).

translate_codon_for_transcript

Translate a codon using the appropriate genetic code for a transcript.

translate_codon_mito

Translate a 3-base codon using the vertebrate mitochondrial genetic code (NCBI table 2).

translate_sequence

Translate a DNA sequence to amino acids, codon by codon.