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"""
File: CodonPostProcessing.py
---------------------------
Post-processing utilities for codon optimization using DNAChisel.
This module provides sequence polishing capabilities to fix restriction sites,
homopolymers, and other constraints while preserving CAI and GC content.
"""
import warnings
import numpy as np
try:
from dnachisel import (
DnaOptimizationProblem,
AvoidPattern,
EnforceGCContent,
EnforceTranslation,
CodonOptimize,
)
DNACHISEL_AVAILABLE = True
except ImportError:
DNACHISEL_AVAILABLE = False
# This warning will be shown when the module is first imported.
warnings.warn(
"DNAChisel is not installed. Post-processing features will be disabled."
)
def polish_sequence_with_dnachisel(
dna_sequence: str,
protein_sequence: str,
gc_bounds: tuple = (45.0, 55.0),
cai_species: str = "e_coli",
avoid_homopolymers_length: int = 6,
enzymes_to_avoid: list = None
):
"""
Polishes a DNA sequence using DNAChisel to meet lab synthesis constraints.
"""
if not DNACHISEL_AVAILABLE:
warnings.warn("DNAChisel not available, skipping post-processing.")
return dna_sequence
if enzymes_to_avoid is None:
# Common cloning enzymes
enzymes_to_avoid = ["EcoRI", "XbaI", "SpeI", "PstI", "NotI"]
try:
# Start with the basic, essential constraints
constraints = [
EnforceTranslation(translation=protein_sequence),
EnforceGCContent(mini=gc_bounds[0] / 100.0, maxi=gc_bounds[1] / 100.0),
]
# Add enzyme avoidance constraints safely
for enzyme in enzymes_to_avoid:
try:
# This is the modern way to avoid enzyme sites
constraints.append(AvoidPattern.from_enzyme_name(enzyme))
except Exception:
warnings.warn(f"Could not find enzyme '{enzyme}' in DNAChisel library.")
# Add homopolymer avoidance constraints
for base in "ATGC":
constraints.append(AvoidPattern(base * avoid_homopolymers_length))
# Define the optimization problem
problem = DnaOptimizationProblem(
sequence=dna_sequence,
constraints=constraints,
objectives=[CodonOptimize(species=cai_species, method="match_codon_usage")]
)
# Solve the problem
problem.resolve_constraints()
problem.optimize()
# Return the polished sequence
return problem.sequence
except Exception as e:
warnings.warn(f"DNAChisel post-processing failed with an error: {e}")
# Return the original sequence if polishing fails
return dna_sequence
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