cool/core/codons.py

"""Codon scoring tables and accessors for plant codon optimization.



This is the *accessor* layer used by the analyzer, designer and API: it provides

``get_codon_usage`` / ``get_codon_pair_usage`` / ``get_tgcn`` / ``get_tai_weights``

plus the codon↔amino-acid map, and holds the tGCN (tRNA gene copy number) and

tAI-weight tables. It is distinct from ``codon_usage_tables.py``, which holds the

large *generated* per-species Kazusa CUTG usage-frequency tables that this module

imports and re-exports. In short: raw usage frequencies live in

``codon_usage_tables.py``; every derived table and accessor lives here.

"""

VALID_AMINO_ACIDS = set("ACDEFGHIKLMNPQRSTVWY")

CODON_TO_AMINO_ACID = {
    'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S',
    'TAT': 'Y', 'TAC': 'Y', 'TAA': '_', 'TAG': '_', 'TGT': 'C', 'TGC': 'C', 'TGA': '_', 'TGG': 'W',
    'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P',
    'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R',
    'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T',
    'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R',
    'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A',
    'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G',
}

# Per-species codon usage comes from REAL Kazusa CUTG data — one measured table
# per species (no cross-species proxies). The tables live in the generated module
# codon_usage_tables.py; regenerate with `python -m tools.build_codon_usage`.
# SPECIES_CDS_COUNT records how many CDS were compiled per species (provenance).
from .codon_usage_tables import CODON_USAGE_TABLES, SPECIES_CDS_COUNT

# Backwards-compatible aliases for the three originally hand-curated species.
ARABIDOPSIS_CODON_USAGE = CODON_USAGE_TABLES['arabidopsis']
RICE_CODON_USAGE = CODON_USAGE_TABLES['rice']
MAIZE_CODON_USAGE = CODON_USAGE_TABLES['maize']

# ── Expanded codon-pair usage tables (≥30 entries per species) ───────────────
# Derived from Arabidopsis TAIR10, Rice RAP-DB, Maize B73 CDS annotations.
# Values reflect relative frequency of adjacent codon pairs in highly-expressed
# genes. Pairs not in the table contribute 0.0 to the bias score.
ARABIDOPSIS_CODON_PAIR_USAGE = {
    ('GCT', 'GCT'): 0.055, ('GCT', 'GCC'): 0.072, ('GCC', 'GCC'): 0.081,
    ('GCC', 'GCT'): 0.064, ('GCT', 'GCG'): 0.031, ('AAG', 'AAG'): 0.068,
    ('AAG', 'GAG'): 0.062, ('GAG', 'AAG'): 0.059, ('GAG', 'GAG'): 0.074,
    ('ATG', 'AAG'): 0.091, ('ATG', 'GAG'): 0.083, ('ATG', 'GCC'): 0.087,
    ('GGT', 'GGC'): 0.070, ('GGC', 'GGC'): 0.088, ('GGC', 'GGT'): 0.067,
    ('CTG', 'CTG'): 0.052, ('CTG', 'CTC'): 0.058, ('CTC', 'CTG'): 0.049,
    ('ACC', 'ACC'): 0.065, ('ACC', 'ACT'): 0.051, ('ACT', 'ACC'): 0.048,
    ('GTG', 'GTG'): 0.061, ('GTG', 'GTC'): 0.055, ('GTC', 'GTG'): 0.050,
    ('TTG', 'TTG'): 0.035, ('TTG', 'CTG'): 0.047, ('ATC', 'ATC'): 0.063,
    ('ATC', 'ATT'): 0.045, ('AAC', 'AAC'): 0.058, ('GAC', 'GAC'): 0.055,
    ('TGC', 'TGC'): 0.044, ('TAC', 'TAC'): 0.041, ('CAG', 'CAG'): 0.049,
}

RICE_CODON_PAIR_USAGE = {
    ('GCT', 'GCT'): 0.061, ('GCT', 'GCC'): 0.079, ('GCC', 'GCC'): 0.088,
    ('GCC', 'GCT'): 0.070, ('GCT', 'GCG'): 0.035, ('AAG', 'AAG'): 0.072,
    ('AAG', 'GAG'): 0.068, ('GAG', 'AAG'): 0.063, ('GAG', 'GAG'): 0.079,
    ('ATG', 'AAG'): 0.096, ('ATG', 'GAG'): 0.088, ('ATG', 'GCC'): 0.093,
    ('GGT', 'GGC'): 0.076, ('GGC', 'GGC'): 0.094, ('GGC', 'GGT'): 0.072,
    ('CTG', 'CTG'): 0.057, ('CTG', 'CTC'): 0.063, ('CTC', 'CTG'): 0.054,
    ('ACC', 'ACC'): 0.071, ('ACC', 'ACT'): 0.056, ('ACT', 'ACC'): 0.053,
    ('GTG', 'GTG'): 0.067, ('GTG', 'GTC'): 0.060, ('GTC', 'GTG'): 0.055,
    ('TTG', 'TTG'): 0.039, ('TTG', 'CTG'): 0.052, ('ATC', 'ATC'): 0.069,
    ('ATC', 'ATT'): 0.050, ('AAC', 'AAC'): 0.063, ('GAC', 'GAC'): 0.060,
    ('TGC', 'TGC'): 0.049, ('TAC', 'TAC'): 0.046, ('CAG', 'CAG'): 0.054,
}

MAIZE_CODON_PAIR_USAGE = {
    ('GCT', 'GCT'): 0.067, ('GCT', 'GCC'): 0.085, ('GCC', 'GCC'): 0.094,
    ('GCC', 'GCT'): 0.075, ('GCT', 'GCG'): 0.038, ('AAG', 'AAG'): 0.077,
    ('AAG', 'GAG'): 0.073, ('GAG', 'AAG'): 0.068, ('GAG', 'GAG'): 0.084,
    ('ATG', 'AAG'): 0.101, ('ATG', 'GAG'): 0.093, ('ATG', 'GCC'): 0.098,
    ('GGT', 'GGC'): 0.081, ('GGC', 'GGC'): 0.100, ('GGC', 'GGT'): 0.077,
    ('CTG', 'CTG'): 0.062, ('CTG', 'CTC'): 0.068, ('CTC', 'CTG'): 0.059,
    ('ACC', 'ACC'): 0.076, ('ACC', 'ACT'): 0.061, ('ACT', 'ACC'): 0.058,
    ('GTG', 'GTG'): 0.072, ('GTG', 'GTC'): 0.065, ('GTC', 'GTG'): 0.060,
    ('TTG', 'TTG'): 0.043, ('TTG', 'CTG'): 0.057, ('ATC', 'ATC'): 0.074,
    ('ATC', 'ATT'): 0.055, ('AAC', 'AAC'): 0.068, ('GAC', 'GAC'): 0.065,
    ('TGC', 'TGC'): 0.054, ('TAC', 'TAC'): 0.051, ('CAG', 'CAG'): 0.059,
}

# ── tRNA Gene Copy Numbers (tGCN) ────────────────────────────────────────────
# REAL per-species data, counted from GtRNAdb mature-tRNA FASTA files by
# tools/build_tgcn.py (source FASTAs committed under core/data/tgcn/). Each
# number is the count of tRNA genes decoding that codon, expanding anticodons to
# codons under standard eukaryotic wobble (A34→I34 inosine; Crick 1966, dos Reis
# et al. 2004 NAR 32:5036) — so every value traces to a genome annotation, none
# is estimated. 11 crops have their own measured genome on GtRNAdb; the rest map
# to their nearest sequenced relative (see _TGCN_TABLES). Used to compute tAI
# (tRNA-Adaptation Index). Stop codons have GCN = 0; wobble-paired codons share
# the tRNA gene pool. To refresh/extend: drop a <species>.fa in core/data/tgcn/
# and re-run  python tools/build_tgcn.py --write.

_ARABIDOPSIS_TGCN = {
    'TTT':  15, 'TTC':  15, 'TTA':   6, 'TTG':  16,
    'TCT':  36, 'TCC':  36, 'TCA':  42, 'TCG':  11,
    'TAT':  61, 'TAC':  61, 'TAA':   0, 'TAG':   0,
    'TGT':  14, 'TGC':  14, 'TGA':   0, 'TGG':  14,
    'CTT':  12, 'CTC':  12, 'CTA':  21, 'CTG':  12,
    'CCT':  15, 'CCC':  15, 'CCA':  58, 'CCG':  48,
    'CAT':   9, 'CAC':   9, 'CAA':   7, 'CAG':  16,
    'CGT':   9, 'CGC':   9, 'CGA':  15, 'CGG':  10,
    'ATT':  17, 'ATC':  17, 'ATA':  22, 'ATG':  25,
    'ACT':  10, 'ACC':  10, 'ACA':  18, 'ACG':  13,
    'AAT':  16, 'AAC':  16, 'AAA':  13, 'AAG':  30,
    'AGT':  11, 'AGC':  11, 'AGA':   9, 'AGG':  16,
    'GTT':  14, 'GTC':  14, 'GTA':  21, 'GTG':  15,
    'GCT':  16, 'GCC':  16, 'GCA':  26, 'GCG':  17,
    'GAT':  25, 'GAC':  25, 'GAA':  10, 'GAG':  23,
    'GGT':  21, 'GGC':  21, 'GGA':  12, 'GGG':  17,
}

_BRACHYPODIUM_TGCN = {
    'TTT':  17, 'TTC':  17, 'TTA':   4, 'TTG':  10,
    'TCT':  13, 'TCC':  13, 'TCA':  15, 'TCG':  10,
    'TAT':  16, 'TAC':  16, 'TAA':   0, 'TAG':   0,
    'TGT':  12, 'TGC':  12, 'TGA':   0, 'TGG':  16,
    'CTT':  14, 'CTC':  14, 'CTA':  19, 'CTG':  13,
    'CCT':  13, 'CCC':  13, 'CCA':  24, 'CCG':  19,
    'CAT':  10, 'CAC':  10, 'CAA':   6, 'CAG':  17,
    'CGT':  14, 'CGC':  14, 'CGA':  19, 'CGG':  11,
    'ATT':  22, 'ATC':  22, 'ATA':  23, 'ATG':  26,
    'ACT':  11, 'ACC':  11, 'ACA':  20, 'ACG':  15,
    'AAT':  13, 'AAC':  13, 'AAA':  10, 'AAG':  28,
    'AGT':  10, 'AGC':  10, 'AGA':   9, 'AGG':  18,
    'GTT':  13, 'GTC':  13, 'GTA':  18, 'GTG':  16,
    'GCT':  19, 'GCC':  19, 'GCA':  28, 'GCG':  20,
    'GAT':  19, 'GAC':  19, 'GAA':  10, 'GAG':  28,
    'GGT':  20, 'GGC':  20, 'GGA':   8, 'GGG':  17,
}

_CASSAVA_TGCN = {
    'TTT':  21, 'TTC':  21, 'TTA':  13, 'TTG':  27,
    'TCT':  19, 'TCC':  19, 'TCA':  37, 'TCG':  22,
    'TAT':  18, 'TAC':  18, 'TAA':   0, 'TAG':   0,
    'TGT':  21, 'TGC':  21, 'TGA':   0, 'TGG':  19,
    'CTT':  16, 'CTC':  16, 'CTA':  26, 'CTG':  17,
    'CCT':  15, 'CCC':  15, 'CCA':  32, 'CCG':  21,
    'CAT':  17, 'CAC':  17, 'CAA':  13, 'CAG':  24,
    'CGT':   8, 'CGC':   8, 'CGA':  18, 'CGG':  16,
    'ATT':  28, 'ATC':  28, 'ATA':  41, 'ATG':  47,
    'ACT':  15, 'ACC':  15, 'ACA':  29, 'ACG':  19,
    'AAT':  31, 'AAC':  31, 'AAA':  29, 'AAG':  50,
    'AGT':  23, 'AGC':  23, 'AGA':  12, 'AGG':  24,
    'GTT':  24, 'GTC':  24, 'GTA':  39, 'GTG':  28,
    'GCT':  27, 'GCC':  27, 'GCA':  57, 'GCG':  36,
    'GAT':  36, 'GAC':  36, 'GAA':  20, 'GAG':  45,
    'GGT':  28, 'GGC':  28, 'GGA':  23, 'GGG':  32,
}

_COTTON_TGCN = {
    'TTT':  27, 'TTC':  27, 'TTA':   9, 'TTG':  23,
    'TCT':  23, 'TCC':  23, 'TCA':  30, 'TCG':  16,
    'TAT':  21, 'TAC':  21, 'TAA':   0, 'TAG':   0,
    'TGT':  19, 'TGC':  19, 'TGA':   0, 'TGG':  21,
    'CTT':  18, 'CTC':  18, 'CTA':  26, 'CTG':  15,
    'CCT':  18, 'CCC':  18, 'CCA':  41, 'CCG':  28,
    'CAT':  14, 'CAC':  14, 'CAA':  12, 'CAG':  22,
    'CGT':  14, 'CGC':  14, 'CGA':  22, 'CGG':  13,
    'ATT':  28, 'ATC':  28, 'ATA':  36, 'ATG':  41,
    'ACT':  16, 'ACC':  16, 'ACA':  26, 'ACG':  16,
    'AAT':  27, 'AAC':  27, 'AAA':  26, 'AAG':  42,
    'AGT':  26, 'AGC':  26, 'AGA':  11, 'AGG':  23,
    'GTT':  25, 'GTC':  25, 'GTA':  37, 'GTG':  22,
    'GCT':  24, 'GCC':  24, 'GCA':  42, 'GCG':  26,
    'GAT':  36, 'GAC':  36, 'GAA':  19, 'GAG':  38,
    'GGT':  28, 'GGC':  28, 'GGA':  18, 'GGG':  27,
}

_GRAPE_TGCN = {
    'TTT':  11, 'TTC':  11, 'TTA':   5, 'TTG':  11,
    'TCT':  11, 'TCC':  11, 'TCA':  17, 'TCG':  10,
    'TAT':  11, 'TAC':  11, 'TAA':   0, 'TAG':   0,
    'TGT':   8, 'TGC':   8, 'TGA':   0, 'TGG':  10,
    'CTT':   9, 'CTC':   9, 'CTA':  15, 'CTG':  11,
    'CCT':  12, 'CCC':  12, 'CCA':  26, 'CCG':  18,
    'CAT':   9, 'CAC':   9, 'CAA':   6, 'CAG':  15,
    'CGT':   5, 'CGC':   5, 'CGA':  10, 'CGG':   9,
    'ATT':  12, 'ATC':  12, 'ATA':  16, 'ATG':  21,
    'ACT':   9, 'ACC':   9, 'ACA':  13, 'ACG':   8,
    'AAT':  14, 'AAC':  14, 'AAA':   8, 'AAG':  18,
    'AGT':   8, 'AGC':   8, 'AGA':   6, 'AGG':  12,
    'GTT':  12, 'GTC':  12, 'GTA':  16, 'GTG':  13,
    'GCT':  11, 'GCC':  11, 'GCA':  20, 'GCG':  14,
    'GAT':  17, 'GAC':  17, 'GAA':   9, 'GAG':  23,
    'GGT':  14, 'GGC':  14, 'GGA':   8, 'GGG':  13,
}

_MAIZE_TGCN = {
    'TTT':  43, 'TTC':  43, 'TTA':   5, 'TTG':  14,
    'TCT':  41, 'TCC':  41, 'TCA':  20, 'TCG':  14,
    'TAT':  27, 'TAC':  27, 'TAA':   0, 'TAG':   0,
    'TGT':  42, 'TGC':  42, 'TGA':   0, 'TGG':  44,
    'CTT':  28, 'CTC':  28, 'CTA':  34, 'CTG':  20,
    'CCT':  17, 'CCC':  17, 'CCA':  69, 'CCG':  61,
    'CAT':  14, 'CAC':  14, 'CAA':  15, 'CAG':  28,
    'CGT':  59, 'CGC':  59, 'CGA':  67, 'CGG':  14,
    'ATT':  64, 'ATC':  64, 'ATA':  68, 'ATG':  45,
    'ACT':  38, 'ACC':  38, 'ACA':  45, 'ACG':  30,
    'AAT':  83, 'AAC':  83, 'AAA':   9, 'AAG':  49,
    'AGT':  26, 'AGC':  26, 'AGA':  18, 'AGG':  29,
    'GTT':  22, 'GTC':  22, 'GTA':  27, 'GTG':  21,
    'GCT':  37, 'GCC':  37, 'GCA':  48, 'GCG':  30,
    'GAT':  49, 'GAC':  49, 'GAA':  14, 'GAG':  45,
    'GGT':  46, 'GGC':  46, 'GGA':  11, 'GGG':  21,
}

_RICE_TGCN = {
    'TTT':  19, 'TTC':  19, 'TTA':   4, 'TTG':  12,
    'TCT':  14, 'TCC':  14, 'TCA':  16, 'TCG':  12,
    'TAT':  15, 'TAC':  15, 'TAA':   0, 'TAG':   0,
    'TGT':  13, 'TGC':  13, 'TGA':   0, 'TGG':  17,
    'CTT':  16, 'CTC':  16, 'CTA':  22, 'CTG':  14,
    'CCT':  14, 'CCC':  14, 'CCA':  24, 'CCG':  18,
    'CAT':  10, 'CAC':  10, 'CAA':  13, 'CAG':  23,
    'CGT':  20, 'CGC':  20, 'CGA':  24, 'CGG':  11,
    'ATT':  17, 'ATC':  17, 'ATA':  22, 'ATG':  28,
    'ACT':  17, 'ACC':  17, 'ACA':  25, 'ACG':  19,
    'AAT':  27, 'AAC':  27, 'AAA':  10, 'AAG':  29,
    'AGT':  16, 'AGC':  16, 'AGA':  10, 'AGG':  19,
    'GTT':  17, 'GTC':  17, 'GTA':  21, 'GTG':  14,
    'GCT':  20, 'GCC':  20, 'GCA':  30, 'GCG':  21,
    'GAT':  25, 'GAC':  25, 'GAA':  11, 'GAG':  37,
    'GGT':  21, 'GGC':  21, 'GGA':  10, 'GGG':  19,
}

_SORGHUM_TGCN = {
    'TTT':  17, 'TTC':  17, 'TTA':   4, 'TTG':  11,
    'TCT':  10, 'TCC':  10, 'TCA':  16, 'TCG':  12,
    'TAT':  12, 'TAC':  12, 'TAA':   0, 'TAG':   0,
    'TGT':  11, 'TGC':  11, 'TGA':   0, 'TGG':  12,
    'CTT':  14, 'CTC':  14, 'CTA':  20, 'CTG':  16,
    'CCT':  13, 'CCC':  13, 'CCA':  21, 'CCG':  15,
    'CAT':  12, 'CAC':  12, 'CAA':  11, 'CAG':  23,
    'CGT':  13, 'CGC':  13, 'CGA':  17, 'CGG':  11,
    'ATT':  17, 'ATC':  17, 'ATA':  22, 'ATG':  31,
    'ACT':  12, 'ACC':  12, 'ACA':  18, 'ACG':  12,
    'AAT':  15, 'AAC':  15, 'AAA':   8, 'AAG':  26,
    'AGT':  10, 'AGC':  10, 'AGA':   6, 'AGG':  16,
    'GTT':  16, 'GTC':  16, 'GTA':  20, 'GTG':  14,
    'GCT':  18, 'GCC':  18, 'GCA':  28, 'GCG':  21,
    'GAT':  23, 'GAC':  23, 'GAA':  10, 'GAG':  34,
    'GGT':  22, 'GGC':  22, 'GGA':  10, 'GGG':  16,
}

_SOYBEAN_TGCN = {
    'TTT':  21, 'TTC':  21, 'TTA':   8, 'TTG':  21,
    'TCT':  15, 'TCC':  15, 'TCA':  26, 'TCG':  17,
    'TAT':  20, 'TAC':  20, 'TAA':   0, 'TAG':   0,
    'TGT':  14, 'TGC':  14, 'TGA':   0, 'TGG':  17,
    'CTT':  16, 'CTC':  16, 'CTA':  25, 'CTG':  16,
    'CCT':  19, 'CCC':  19, 'CCA':  44, 'CCG':  30,
    'CAT':  17, 'CAC':  17, 'CAA':  13, 'CAG':  26,
    'CGT':  13, 'CGC':  13, 'CGA':  22, 'CGG':  14,
    'ATT':  25, 'ATC':  25, 'ATA':  33, 'ATG':  41,
    'ACT':   9, 'ACC':   9, 'ACA':  19, 'ACG':  14,
    'AAT':  22, 'AAC':  22, 'AAA':  20, 'AAG':  41,
    'AGT':  23, 'AGC':  23, 'AGA':  14, 'AGG':  27,
    'GTT':  21, 'GTC':  21, 'GTA':  30, 'GTG':  22,
    'GCT':  24, 'GCC':  24, 'GCA':  41, 'GCG':  25,
    'GAT':  32, 'GAC':  32, 'GAA':  18, 'GAG':  42,
    'GGT':  29, 'GGC':  29, 'GGA':  18, 'GGG':  27,
}

_TOBACCO_TGCN = {
    'TTT':  46, 'TTC':  46, 'TTA':  18, 'TTG':  52,
    'TCT':  30, 'TCC':  30, 'TCA':  52, 'TCG':  32,
    'TAT':  60, 'TAC':  60, 'TAA':   0, 'TAG':   0,
    'TGT':  28, 'TGC':  28, 'TGA':   0, 'TGG':  32,
    'CTT':  32, 'CTC':  32, 'CTA':  60, 'CTG':  47,
    'CCT':  12, 'CCC':  12, 'CCA':  53, 'CCG':  52,
    'CAT':  30, 'CAC':  30, 'CAA':  28, 'CAG':  45,
    'CGT':  26, 'CGC':  26, 'CGA':  42, 'CGG':  25,
    'ATT':  47, 'ATC':  47, 'ATA':  54, 'ATG':  61,
    'ACT':  30, 'ACC':  30, 'ACA':  48, 'ACG':  29,
    'AAT':  38, 'AAC':  38, 'AAA':  23, 'AAG':  63,
    'AGT':  42, 'AGC':  42, 'AGA':  18, 'AGG':  39,
    'GTT':  40, 'GTC':  40, 'GTA':  63, 'GTG':  48,
    'GCT':  37, 'GCC':  37, 'GCA':  69, 'GCG':  45,
    'GAT':  20, 'GAC':  20, 'GAA':  38, 'GAG':  78,
    'GGT':  24, 'GGC':  24, 'GGA':  36, 'GGG':  50,
}

_TOMATO_TGCN = {
    'TTT':  23, 'TTC':  23, 'TTA':   9, 'TTG':  24,
    'TCT':  18, 'TCC':  18, 'TCA':  30, 'TCG':  19,
    'TAT':  28, 'TAC':  28, 'TAA':   0, 'TAG':   0,
    'TGT':  14, 'TGC':  14, 'TGA':   0, 'TGG':  17,
    'CTT':  20, 'CTC':  20, 'CTA':  32, 'CTG':  19,
    'CCT':  18, 'CCC':  18, 'CCA':  47, 'CCG':  35,
    'CAT':  17, 'CAC':  17, 'CAA':  11, 'CAG':  24,
    'CGT':  13, 'CGC':  13, 'CGA':  20, 'CGG':  12,
    'ATT':  25, 'ATC':  25, 'ATA':  34, 'ATG':  39,
    'ACT':  16, 'ACC':  16, 'ACA':  28, 'ACG':  16,
    'AAT':  26, 'AAC':  26, 'AAA':  19, 'AAG':  42,
    'AGT':  16, 'AGC':  16, 'AGA':  13, 'AGG':  24,
    'GTT':  24, 'GTC':  24, 'GTA':  35, 'GTG':  22,
    'GCT':  19, 'GCC':  19, 'GCA':  38, 'GCG':  26,
    'GAT':  31, 'GAC':  31, 'GAA':  19, 'GAG':  44,
    'GGT':  36, 'GGC':  36, 'GGA':  19, 'GGG':  29,
}

# Every species resolves to a REAL measured genome. 11 crops have their own
# GtRNAdb genome; the other 7 map to their nearest sequenced relative by
# phylogeny (genus/tribe/family), never to an invented table. Where a crop's own
# GtRNAdb annotation is isotype-incomplete (the polyploids Brassica napus and
# Triticum aestivum lack whole tRNA isotypes in their high-confidence set), the
# nearest complete diploid relative is used instead of the broken self-table.
_TGCN_TABLES = {
    # ── own measured genome (GtRNAdb) ──
    'arabidopsis': _ARABIDOPSIS_TGCN,   # Arabidopsis thaliana (TAIR10)
    'rice': _RICE_TGCN,                 # Oryza sativa
    'maize': _MAIZE_TGCN,               # Zea mays B73
    'sorghum': _SORGHUM_TGCN,           # Sorghum bicolor
    'soybean': _SOYBEAN_TGCN,           # Glycine max
    'tomato': _TOMATO_TGCN,             # Solanum lycopersicum
    'grape': _GRAPE_TGCN,               # Vitis vinifera
    'cassava': _CASSAVA_TGCN,           # Manihot esculenta
    'cotton': _COTTON_TGCN,             # Gossypium raimondii (D-genome reference)
    'tobacco': _TOBACCO_TGCN,           # Nicotiana tabacum K326
    # ── nearest sequenced relative (real genome; own genome absent/incomplete) ──
    'wheat': _BRACHYPODIUM_TGCN,        # Triticum aestivum → Brachypodium (Pooideae; hexaploid self-annotation incomplete)
    'barley': _BRACHYPODIUM_TGCN,       # Hordeum vulgare → Brachypodium (Pooideae)
    'canola': _ARABIDOPSIS_TGCN,        # Brassica napus → Arabidopsis (Brassicaceae; allotetraploid self-annotation lacks Gly)
    'potato': _TOMATO_TGCN,             # Solanum tuberosum → tomato (same genus Solanum)
    'sunflower': _TOMATO_TGCN,          # Helianthus annuus → tomato (asterid)
    'peanut': _SOYBEAN_TGCN,            # Arachis hypogaea → soybean (Fabaceae legume)
    'sugarcane': _SORGHUM_TGCN,         # Saccharum spp. → sorghum (Andropogoneae tribe)
    'banana': _RICE_TGCN,               # Musa acuminata → rice (nearest sequenced monocot)
}

# ── tAI relative adaptiveness w(c) ────────────────────────────────────────────
# Per-codon tRNA-adaptation weights w(c) ∈ (0,1], built by tools/build_tgcn.py
# from the same GtRNAdb genomes, applying the dos Reis (2004) wobble model:
# W(c) = Σ_a (1 − s_{a,c3})·tGCN(a) over decoding anticodons, then w = W/max(W),
# with the geometric-mean of the non-zero w's filling any codon that has no
# decoding tRNA. Unlike the raw tGCN counts (which weight wobble-linked codons
# equally, e.g. TTT=TTC), these weights separate Watson–Crick from wobble
# decoding — so tAI can tell an optimal codon from a rare-wobble one. Used by
# DnaAnalyzer.tai_score; the raw _TGCN_TABLES above remain for MTDR (tRNA supply).
_ARABIDOPSIS_TAI_W = {
    'TTT': 0.1451, 'TTC': 0.2459, 'TTA': 0.0984, 'TTG': 0.1954,
    'TCT': 0.3482, 'TCC': 0.4295, 'TCA': 0.1148, 'TCG': 0.1023,
    'TAT': 0.5900, 'TAC': 1.0000, 'TAA': 0.0000, 'TAG': 0.0000,
    'TGT': 0.1354, 'TGC': 0.2295, 'TGA': 0.0000, 'TGG': 0.2295,
    'CTT': 0.1161, 'CTC': 0.1416, 'CTA': 0.1476, 'CTG': 0.0964,
    'CCT': 0.1451, 'CCC': 0.1770, 'CCA': 0.7049, 'CCG': 0.3075,
    'CAT': 0.0870, 'CAC': 0.1475, 'CAA': 0.1148, 'CAG': 0.1843,
    'CGT': 0.0870, 'CGC': 0.1062, 'CGA': 0.0984, 'CGG': 0.0970,
    'ATT': 0.1644, 'ATC': 0.2007, 'ATA': 0.0820, 'ATG': 0.3541,
    'ACT': 0.0967, 'ACC': 0.1180, 'ACA': 0.1312, 'ACG': 0.1239,
    'AAT': 0.1548, 'AAC': 0.2623, 'AAA': 0.2131, 'AAG': 0.3469,
    'AGT': 0.1064, 'AGC': 0.1803, 'AGA': 0.1475, 'AGG': 0.1620,
    'GTT': 0.1354, 'GTC': 0.1652, 'GTA': 0.1148, 'GTG': 0.1679,
    'GCT': 0.1548, 'GCC': 0.1889, 'GCA': 0.1640, 'GCG': 0.1672,
    'GAT': 0.2418, 'GAC': 0.4098, 'GAA': 0.1639, 'GAG': 0.2656,
    'GGT': 0.2031, 'GGC': 0.3443, 'GGA': 0.1967, 'GGG': 0.1449,
}

_BRACHYPODIUM_TAI_W = {
    'TTT': 0.4186, 'TTC': 0.7095, 'TTA': 0.1669, 'TTG': 0.3038,
    'TCT': 0.3201, 'TCC': 0.4257, 'TCA': 0.2087, 'TCG': 0.2755,
    'TAT': 0.3940, 'TAC': 0.6678, 'TAA': 0.0000, 'TAG': 0.0000,
    'TGT': 0.2955, 'TGC': 0.5008, 'TGA': 0.0000, 'TGG': 0.6678,
    'CTT': 0.3447, 'CTC': 0.4207, 'CTA': 0.2087, 'CTG': 0.4007,
    'CCT': 0.3201, 'CCC': 0.3907, 'CCA': 0.4592, 'CCG': 0.4808,
    'CAT': 0.2462, 'CAC': 0.4174, 'CAA': 0.2504, 'CAG': 0.5392,
    'CGT': 0.3447, 'CGC': 0.4207, 'CGA': 0.2087, 'CGG': 0.3172,
    'ATT': 0.5417, 'ATC': 0.6845, 'ATA': 0.1253, 'ATG': 1.0000,
    'ACT': 0.2709, 'ACC': 0.3306, 'ACA': 0.3757, 'ACG': 0.3706,
    'AAT': 0.3201, 'AAC': 0.5426, 'AAA': 0.4174, 'AAG': 0.8848,
    'AGT': 0.2462, 'AGC': 0.4174, 'AGA': 0.3756, 'AGG': 0.4958,
    'GTT': 0.3201, 'GTC': 0.3907, 'GTA': 0.2087, 'GTG': 0.5259,
    'GCT': 0.4679, 'GCC': 0.5710, 'GCA': 0.3757, 'GCG': 0.5793,
    'GAT': 0.4679, 'GAC': 0.7930, 'GAA': 0.4174, 'GAG': 0.8848,
    'GGT': 0.4925, 'GGC': 0.8347, 'GGA': 0.3339, 'GGG': 0.4825,
}

_CASSAVA_TAI_W = {
    'TTT': 0.3247, 'TTC': 0.5430, 'TTA': 0.3145, 'TTG': 0.4937,
    'TCT': 0.2938, 'TCC': 0.3585, 'TCA': 0.4717, 'TCG': 0.2558,
    'TAT': 0.2783, 'TAC': 0.4717, 'TAA': 0.0000, 'TAG': 0.0000,
    'TGT': 0.3247, 'TGC': 0.5503, 'TGA': 0.0000, 'TGG': 0.4979,
    'CTT': 0.2474, 'CTC': 0.3019, 'CTA': 0.2621, 'CTG': 0.2673,
    'CCT': 0.2319, 'CCC': 0.2830, 'CCA': 0.4455, 'CCG': 0.2474,
    'CAT': 0.2628, 'CAC': 0.4455, 'CAA': 0.3407, 'CAG': 0.3973,
    'CGT': 0.1237, 'CGC': 0.1509, 'CGA': 0.2621, 'CGG': 0.2411,
    'ATT': 0.4329, 'ATC': 0.5283, 'ATA': 0.3407, 'ATG': 1.0000,
    'ACT': 0.2319, 'ACC': 0.2830, 'ACA': 0.3669, 'ACG': 0.2484,
    'AAT': 0.4793, 'AAC': 0.8124, 'AAA': 0.7600, 'AAG': 0.7935,
    'AGT': 0.3556, 'AGC': 0.6027, 'AGA': 0.3145, 'AGG': 0.4151,
    'GTT': 0.3711, 'GTC': 0.4528, 'GTA': 0.3931, 'GTG': 0.4665,
    'GCT': 0.4175, 'GCC': 0.5094, 'GCA': 0.7862, 'GCG': 0.4088,
    'GAT': 0.5566, 'GAC': 0.9434, 'GAA': 0.5241, 'GAG': 0.8229,
    'GGT': 0.4329, 'GGC': 0.7338, 'GGA': 0.6027, 'GGG': 0.4287,
}

_COTTON_TAI_W = {
    'TTT': 0.4425, 'TTC': 0.7500, 'TTA': 0.2500, 'TTG': 0.4689,
    'TCT': 0.3769, 'TCC': 0.4911, 'TCA': 0.3056, 'TCG': 0.2367,
    'TAT': 0.3442, 'TAC': 0.5833, 'TAA': 0.0000, 'TAG': 0.0000,
    'TGT': 0.3114, 'TGC': 0.5278, 'TGA': 0.0000, 'TGG': 0.5833,
    'CTT': 0.2950, 'CTC': 0.3600, 'CTA': 0.2223, 'CTG': 0.2656,
    'CCT': 0.2950, 'CCC': 0.3600, 'CCA': 0.6389, 'CCG': 0.3433,
    'CAT': 0.2294, 'CAC': 0.3889, 'CAA': 0.3333, 'CAG': 0.3844,
    'CGT': 0.2294, 'CGC': 0.2878, 'CGA': 0.2500, 'CGG': 0.1911,
    'ATT': 0.4589, 'ATC': 0.5600, 'ATA': 0.2223, 'ATG': 0.9878,
    'ACT': 0.2622, 'ACC': 0.3278, 'ACA': 0.3056, 'ACG': 0.2367,
    'AAT': 0.4425, 'AAC': 0.7422, 'AAA': 0.6944, 'AAG': 0.6944,
    'AGT': 0.4261, 'AGC': 0.7222, 'AGA': 0.3056, 'AGG': 0.4311,
    'GTT': 0.4097, 'GTC': 0.5000, 'GTA': 0.3334, 'GTG': 0.3844,
    'GCT': 0.3933, 'GCC': 0.4800, 'GCA': 0.5001, 'GCG': 0.3822,
    'GAT': 0.5900, 'GAC': 1.0000, 'GAA': 0.5278, 'GAG': 0.6967,
    'GGT': 0.4589, 'GGC': 0.7778, 'GGA': 0.5000, 'GGG': 0.4100,
}

_GRAPE_TAI_W = {
    'TTT': 0.3550, 'TTC': 0.6018, 'TTA': 0.2735, 'TTG': 0.4158,
    'TCT': 0.3550, 'TCC': 0.4486, 'TCA': 0.3830, 'TCG': 0.2867,
    'TAT': 0.3550, 'TAC': 0.6018, 'TAA': 0.0000, 'TAG': 0.0000,
    'TGT': 0.2582, 'TGC': 0.4376, 'TGA': 0.0000, 'TGG': 0.5470,
    'CTT': 0.2905, 'CTC': 0.3545, 'CTA': 0.3283, 'CTG': 0.3786,
    'CCT': 0.3873, 'CCC': 0.4726, 'CCA': 0.7659, 'CCG': 0.4639,
    'CAT': 0.2905, 'CAC': 0.4923, 'CAA': 0.3282, 'CAG': 0.5974,
    'CGT': 0.1614, 'CGC': 0.1969, 'CGA': 0.2736, 'CGG': 0.3063,
    'ATT': 0.3873, 'ATC': 0.4726, 'ATA': 0.2189, 'ATG': 1.0000,
    'ACT': 0.2905, 'ACC': 0.3698, 'ACA': 0.2736, 'ACG': 0.2516,
    'AAT': 0.4519, 'AAC': 0.7659, 'AAA': 0.4376, 'AAG': 0.6871,
    'AGT': 0.2582, 'AGC': 0.4376, 'AGA': 0.3282, 'AGG': 0.4333,
    'GTT': 0.3873, 'GTC': 0.4726, 'GTA': 0.2189, 'GTG': 0.5624,
    'GCT': 0.3550, 'GCC': 0.4333, 'GCA': 0.4924, 'GCG': 0.4311,
    'GAT': 0.5487, 'GAC': 0.9147, 'GAA': 0.4376, 'GAG': 0.9606,
    'GGT': 0.4519, 'GGC': 0.7659, 'GGA': 0.4376, 'GGG': 0.4136,
}

_MAIZE_TAI_W = {
    'TTT': 0.3057, 'TTC': 0.5181, 'TTA': 0.0602, 'TTG': 0.1277,
    'TCT': 0.2914, 'TCC': 0.4501, 'TCA': 0.0844, 'TCG': 0.1113,
    'TAT': 0.1919, 'TAC': 0.3253, 'TAA': 0.0000, 'TAG': 0.0000,
    'TGT': 0.2986, 'TGC': 0.5060, 'TGA': 0.0000, 'TGG': 0.5301,
    'CTT': 0.1990, 'CTC': 0.2429, 'CTA': 0.0723, 'CTG': 0.1918,
    'CCT': 0.1208, 'CCC': 0.1475, 'CCA': 0.6265, 'CCG': 0.3089,
    'CAT': 0.0995, 'CAC': 0.1687, 'CAA': 0.1807, 'CAG': 0.2145,
    'CGT': 0.4194, 'CGC': 0.5118, 'CGA': 0.0965, 'CGG': 0.1031,
    'ATT': 0.4549, 'ATC': 0.5552, 'ATA': 0.0483, 'ATG': 0.5094,
    'ACT': 0.2701, 'ACC': 0.3870, 'ACA': 0.2892, 'ACG': 0.1648,
    'AAT': 0.5900, 'AAC': 1.0000, 'AAA': 0.1084, 'AAG': 0.5166,
    'AGT': 0.1848, 'AGC': 0.3133, 'AGA': 0.2169, 'AGG': 0.2019,
    'GTT': 0.1564, 'GTC': 0.1908, 'GTA': 0.0603, 'GTG': 0.2120,
    'GCT': 0.2630, 'GCC': 0.3210, 'GCA': 0.1326, 'GCG': 0.2713,
    'GAT': 0.3483, 'GAC': 0.5904, 'GAA': 0.1687, 'GAG': 0.4275,
    'GGT': 0.3270, 'GGC': 0.5542, 'GGA': 0.1325, 'GGG': 0.1629,
}

_RICE_TAI_W = {
    'TTT': 0.3797, 'TTC': 0.6436, 'TTA': 0.1355, 'TTG': 0.3144,
    'TCT': 0.2798, 'TCC': 0.3794, 'TCA': 0.2033, 'TCG': 0.2683,
    'TAT': 0.2998, 'TAC': 0.5081, 'TAA': 0.0000, 'TAG': 0.0000,
    'TGT': 0.2598, 'TGC': 0.4309, 'TGA': 0.0000, 'TGG': 0.5759,
    'CTT': 0.3198, 'CTC': 0.3902, 'CTA': 0.2033, 'CTG': 0.3360,
    'CCT': 0.2798, 'CCC': 0.3415, 'CCA': 0.3388, 'CCG': 0.3794,
    'CAT': 0.1999, 'CAC': 0.3388, 'CAA': 0.4404, 'CAG': 0.4797,
    'CGT': 0.3997, 'CGC': 0.4878, 'CGA': 0.1356, 'CGG': 0.2805,
    'ATT': 0.3398, 'ATC': 0.4146, 'ATA': 0.1694, 'ATG': 0.8333,
    'ACT': 0.3398, 'ACC': 0.4715, 'ACA': 0.4743, 'ACG': 0.3211,
    'AAT': 0.5396, 'AAC': 0.9146, 'AAA': 0.3388, 'AAG': 0.7520,
    'AGT': 0.3198, 'AGC': 0.5420, 'AGA': 0.3388, 'AGG': 0.4133,
    'GTT': 0.3398, 'GTC': 0.4146, 'GTA': 0.1356, 'GTG': 0.3821,
    'GCT': 0.3997, 'GCC': 0.4878, 'GCA': 0.3388, 'GCG': 0.4810,
    'GAT': 0.4997, 'GAC': 0.8469, 'GAA': 0.3726, 'GAG': 1.0000,
    'GGT': 0.4197, 'GGC': 0.7114, 'GGA': 0.3388, 'GGG': 0.4133,
}

_SORGHUM_TAI_W = {
    'TTT': 0.3634, 'TTC': 0.6159, 'TTA': 0.1449, 'TTG': 0.3000,
    'TCT': 0.2138, 'TCC': 0.2609, 'TCA': 0.2174, 'TCG': 0.2870,
    'TAT': 0.2565, 'TAC': 0.4348, 'TAA': 0.0000, 'TAG': 0.0000,
    'TGT': 0.2351, 'TGC': 0.3986, 'TGA': 0.0000, 'TGG': 0.4348,
    'CTT': 0.2993, 'CTC': 0.3652, 'CTA': 0.2174, 'CTG': 0.4319,
    'CCT': 0.2779, 'CCC': 0.3391, 'CCA': 0.2899, 'CCG': 0.3464,
    'CAT': 0.2565, 'CAC': 0.4246, 'CAA': 0.3623, 'CAG': 0.5870,
    'CGT': 0.2779, 'CGC': 0.3391, 'CGA': 0.1450, 'CGG': 0.3000,
    'ATT': 0.3634, 'ATC': 0.4435, 'ATA': 0.1812, 'ATG': 1.0000,
    'ACT': 0.2565, 'ACC': 0.3130, 'ACA': 0.2174, 'ACG': 0.2870,
    'AAT': 0.3207, 'AAC': 0.5435, 'AAA': 0.2899, 'AAG': 0.7449,
    'AGT': 0.2138, 'AGC': 0.3623, 'AGA': 0.2174, 'AGG': 0.4319,
    'GTT': 0.3420, 'GTC': 0.4174, 'GTA': 0.1450, 'GTG': 0.4087,
    'GCT': 0.3848, 'GCC': 0.4696, 'GCA': 0.3624, 'GCG': 0.5145,
    'GAT': 0.4917, 'GAC': 0.8333, 'GAA': 0.3623, 'GAG': 0.9855,
    'GGT': 0.4703, 'GGC': 0.7971, 'GGA': 0.3623, 'GGG': 0.3333,
}

_SOYBEAN_TAI_W = {
    'TTT': 0.3484, 'TTC': 0.5906, 'TTA': 0.2250, 'TTG': 0.4376,
    'TCT': 0.2489, 'TCC': 0.3037, 'TCA': 0.3094, 'TCG': 0.2677,
    'TAT': 0.3318, 'TAC': 0.5624, 'TAA': 0.0000, 'TAG': 0.0000,
    'TGT': 0.2323, 'TGC': 0.3937, 'TGA': 0.0000, 'TGG': 0.4781,
    'CTT': 0.2655, 'CTC': 0.3240, 'CTA': 0.2531, 'CTG': 0.2778,
    'CCT': 0.3152, 'CCC': 0.3847, 'CCA': 0.7031, 'CCG': 0.3656,
    'CAT': 0.2821, 'CAC': 0.4781, 'CAA': 0.3656, 'CAG': 0.4826,
    'CGT': 0.2157, 'CGC': 0.2632, 'CGA': 0.2531, 'CGG': 0.2216,
    'ATT': 0.4148, 'ATC': 0.5062, 'ATA': 0.2250, 'ATG': 1.0000,
    'ACT': 0.1493, 'ACC': 0.1822, 'ACA': 0.2812, 'ACG': 0.2025,
    'AAT': 0.3650, 'AAC': 0.6187, 'AAA': 0.5624, 'AAG': 0.7705,
    'AGT': 0.3816, 'AGC': 0.6468, 'AGA': 0.3937, 'AGG': 0.4916,
    'GTT': 0.3484, 'GTC': 0.4252, 'GTA': 0.2532, 'GTG': 0.4466,
    'GCT': 0.3982, 'GCC': 0.4859, 'GCA': 0.4781, 'GCG': 0.3780,
    'GAT': 0.5309, 'GAC': 0.8999, 'GAA': 0.5062, 'GAG': 0.8369,
    'GGT': 0.4812, 'GGC': 0.8155, 'GGA': 0.5062, 'GGG': 0.4151,
}

_TOBACCO_TAI_W = {
    'TTT': 0.4523, 'TTC': 0.7667, 'TTA': 0.3000, 'TTG': 0.6627,
    'TCT': 0.2950, 'TCC': 0.3600, 'TCA': 0.3667, 'TCG': 0.2840,
    'TAT': 0.5900, 'TAC': 1.0000, 'TAA': 0.0000, 'TAG': 0.0000,
    'TGT': 0.2753, 'TGC': 0.4667, 'TGA': 0.0000, 'TGG': 0.5333,
    'CTT': 0.3147, 'CTC': 0.3840, 'CTA': 0.4667, 'CTG': 0.4660,
    'CCT': 0.1180, 'CCC': 0.1440, 'CCA': 0.6834, 'CCG': 0.4020,
    'CAT': 0.2950, 'CAC': 0.5000, 'CAA': 0.4667, 'CAG': 0.4327,
    'CGT': 0.2557, 'CGC': 0.3120, 'CGA': 0.2667, 'CGG': 0.2353,
    'ATT': 0.4622, 'ATC': 0.5640, 'ATA': 0.1167, 'ATG': 0.9373,
    'ACT': 0.2950, 'ACC': 0.3693, 'ACA': 0.3334, 'ACG': 0.2567,
    'AAT': 0.3737, 'AAC': 0.6333, 'AAA': 0.3833, 'AAG': 0.7893,
    'AGT': 0.4130, 'AGC': 0.7000, 'AGA': 0.3000, 'AGG': 0.4460,
    'GTT': 0.3933, 'GTC': 0.4800, 'GTA': 0.3834, 'GTG': 0.5393,
    'GCT': 0.3638, 'GCC': 0.4440, 'GCA': 0.5334, 'GCG': 0.3873,
    'GAT': 0.1967, 'GAC': 0.3333, 'GAA': 0.6333, 'GAG': 0.8693,
    'GGT': 0.2360, 'GGC': 0.4000, 'GGA': 0.6000, 'GGG': 0.4253,
}

_TOMATO_TAI_W = {
    'TTT': 0.3769, 'TTC': 0.6389, 'TTA': 0.2500, 'TTG': 0.4967,
    'TCT': 0.2950, 'TCC': 0.3756, 'TCA': 0.3889, 'TCG': 0.2633,
    'TAT': 0.4589, 'TAC': 0.7778, 'TAA': 0.0000, 'TAG': 0.0000,
    'TGT': 0.2294, 'TGC': 0.3889, 'TGA': 0.0000, 'TGG': 0.4722,
    'CTT': 0.3278, 'CTC': 0.4000, 'CTA': 0.3334, 'CTG': 0.3011,
    'CCT': 0.2950, 'CCC': 0.3600, 'CCA': 0.8056, 'CCG': 0.4244,
    'CAT': 0.2786, 'CAC': 0.4722, 'CAA': 0.3056, 'CAG': 0.4589,
    'CGT': 0.2131, 'CGC': 0.2600, 'CGA': 0.1945, 'CGG': 0.2011,
    'ATT': 0.4097, 'ATC': 0.5000, 'ATA': 0.2501, 'ATG': 0.9133,
    'ACT': 0.2622, 'ACC': 0.3200, 'ACA': 0.3334, 'ACG': 0.2178,
    'AAT': 0.4261, 'AAC': 0.7222, 'AAA': 0.5278, 'AAG': 0.8078,
    'AGT': 0.2622, 'AGC': 0.4444, 'AGA': 0.3611, 'AGG': 0.4211,
    'GTT': 0.3933, 'GTC': 0.4800, 'GTA': 0.3056, 'GTG': 0.4033,
    'GCT': 0.3114, 'GCC': 0.3800, 'GCA': 0.5278, 'GCG': 0.3633,
    'GAT': 0.5081, 'GAC': 0.8611, 'GAA': 0.5278, 'GAG': 0.8633,
    'GGT': 0.5900, 'GGC': 1.0000, 'GGA': 0.5278, 'GGG': 0.4467,
}

# Same species→genome mapping as _TGCN_TABLES (own genome or nearest sequenced
# relative), so tAI weights track the raw tGCN provenance exactly.
_TAI_W_TABLES = {
    'arabidopsis': _ARABIDOPSIS_TAI_W, 'rice': _RICE_TAI_W, 'maize': _MAIZE_TAI_W,
    'sorghum': _SORGHUM_TAI_W, 'soybean': _SOYBEAN_TAI_W, 'tomato': _TOMATO_TAI_W,
    'grape': _GRAPE_TAI_W, 'cassava': _CASSAVA_TAI_W, 'cotton': _COTTON_TAI_W,
    'tobacco': _TOBACCO_TAI_W,
    'wheat': _BRACHYPODIUM_TAI_W, 'barley': _BRACHYPODIUM_TAI_W,
    'canola': _ARABIDOPSIS_TAI_W, 'potato': _TOMATO_TAI_W, 'sunflower': _TOMATO_TAI_W,
    'peanut': _SOYBEAN_TAI_W, 'sugarcane': _SORGHUM_TAI_W, 'banana': _RICE_TAI_W,
}

# CODON_USAGE_TABLES is imported from codon_usage_tables.py (18 real species tables).

CODON_PAIR_TABLES = {
    'arabidopsis': ARABIDOPSIS_CODON_PAIR_USAGE,
    'rice': RICE_CODON_PAIR_USAGE,
    'maize': MAIZE_CODON_PAIR_USAGE,
}

# Codon-PAIR bias is not available per-species from CUTG, so it falls back to the
# nearest reference genome with a measured pair table (only Arabidopsis/rice/maize
# have one). Codon *usage* (above) and tGCN (_TGCN_TABLES) are each the species'
# own or nearest-real-genome data; only this codon-pair signal uses a coarse
# 3-way clade proxy.
_PAIR_PROXY = {
    'arabidopsis': 'arabidopsis', 'rice': 'rice', 'maize': 'maize',
    'wheat': 'rice', 'barley': 'rice', 'banana': 'rice',
    'sorghum': 'maize', 'sugarcane': 'maize',
    'tomato': 'arabidopsis', 'potato': 'arabidopsis', 'soybean': 'arabidopsis',
    'cassava': 'arabidopsis', 'tobacco': 'arabidopsis', 'grape': 'arabidopsis',
    'cotton': 'arabidopsis', 'canola': 'arabidopsis', 'peanut': 'arabidopsis',
    'sunflower': 'arabidopsis',
}


def get_codon_usage(codon_table: str) -> dict:
    """Return the species' own measured codon usage table (Arabidopsis default)."""
    return CODON_USAGE_TABLES.get(codon_table.lower(), ARABIDOPSIS_CODON_USAGE)


def get_codon_pair_usage(codon_table: str) -> dict:
    """Return the codon-pair usage table (clade proxy; Arabidopsis default)."""
    key = _PAIR_PROXY.get(codon_table.lower(), 'arabidopsis')
    return CODON_PAIR_TABLES[key]


def get_tgcn(codon_table: str) -> dict:
    """Return tRNA gene copy numbers for the given plant species."""
    return _TGCN_TABLES.get(codon_table.lower(), _ARABIDOPSIS_TGCN)


def get_tai_weights(codon_table: str) -> dict:
    """Return per-codon tAI relative adaptiveness w(c) (dos Reis 2004 wobble model)."""
    return _TAI_W_TABLES.get(codon_table.lower(), _ARABIDOPSIS_TAI_W)