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4533472 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 | #!/usr/bin/env python3
"""Reproduce a single-nucleotide stop-context derivation."""
from __future__ import annotations
import argparse
import json
STOPS = {"TAA", "TAG", "TGA"}
def derive(wild_type_codon: str, codon_position: int, alternate: str, plus_four: str):
codon = wild_type_codon.upper()
if len(codon) != 3 or any(base not in "ACGT" for base in codon):
raise ValueError("wild-type codon must be three A/C/G/T bases")
if codon_position not in {1, 2, 3}:
raise ValueError("codon position must be 1, 2, or 3")
if alternate.upper() not in "ACGT" or plus_four.upper() not in "ACGT":
raise ValueError("alternate and +4 base must each be A/C/G/T")
mutant = list(codon)
mutant[codon_position - 1] = alternate.upper()
mutant_codon = "".join(mutant)
return {
"wild_type_codon": codon,
"mutant_codon": mutant_codon,
"is_stop": mutant_codon in STOPS,
"dna_context": f"{mutant_codon}-{plus_four.upper()}",
"rna_context": f"{mutant_codon.replace('T', 'U')}-{plus_four.upper().replace('T', 'U')}",
}
def main() -> None:
parser = argparse.ArgumentParser()
parser.add_argument("--wild-type-codon", required=True)
parser.add_argument("--codon-position", required=True, type=int)
parser.add_argument("--alternate", required=True)
parser.add_argument("--plus-four", required=True)
args = parser.parse_args()
print(json.dumps(derive(args.wild_type_codon, args.codon_position, args.alternate, args.plus_four), indent=2))
if __name__ == "__main__":
main()
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