| |
| """ |
| Script to design oligos using MultiAssemblyDesigner. |
| |
| Example usage: |
| |
| conda activate multievolve |
| |
| p3_assembly_design.py \ |
| --mutations-file multievolve_proposals.csv \ |
| --wt-fasta APEX_33overhang.fasta \ |
| --overhang 33 \ |
| --species human \ |
| --oligo-direction bottom \ |
| --tm 80 \ |
| --output design |
| """ |
|
|
| import argparse |
| import sys |
| import pandas as pd |
|
|
| def parse_args(): |
| """Parse command line arguments.""" |
| parser = argparse.ArgumentParser(description='Design oligos using MultiAssemblyDesigner') |
| |
| parser.add_argument( |
| '-m', |
| '--mutations-file', |
| required=True, |
| help='Path to CSV file containing mutations (no header)' |
| ) |
| |
| parser.add_argument( |
| '-wt', |
| '--wt-fasta', |
| required=True, |
| help='Path to input FASTA file' |
| ) |
| |
| parser.add_argument( |
| '-ov', |
| '--overhang', |
| type=int, |
| default=33, |
| help='Overhang length (default: 33)' |
| ) |
| |
| parser.add_argument( |
| '-s', |
| '--species', |
| choices=['human', 'ecoli', 'yeast'], |
| default='human', |
| help='Species (default: human)' |
| ) |
| |
| parser.add_argument( |
| '-d', |
| '--oligo-direction', |
| choices=['top', 'bottom'], |
| default='bottom', |
| help='Oligo direction (default: bottom)' |
| ) |
| |
| parser.add_argument( |
| '--tm', |
| type=float, |
| default=80.0, |
| help='Melting temperature (default: 80.0)' |
| ) |
|
|
| parser.add_argument( |
| '-o', |
| '--output', |
| choices=['design', 'update'], |
| default='design', |
| help='Output type (default: design)' |
| ) |
| |
| return parser.parse_args() |
|
|
| def main(): |
| """Main function.""" |
| |
| args = parse_args() |
| |
| |
| try: |
| from model import MultiAssemblyDesigner |
| except ImportError as e: |
| print(f"Error importing MultiAssemblyDesigner: {e}") |
| print("Make sure the src directory path is correct and contains the required module") |
| sys.exit(1) |
| |
| |
| try: |
| df = pd.read_csv(args.mutations_file, header=None) |
| except Exception as e: |
| print(f"Error reading mutations file: {e}") |
| sys.exit(1) |
| |
| |
| try: |
| designer = MultiAssemblyDesigner( |
| df, |
| args.wt_fasta, |
| args.overhang, |
| args.species, |
| oligo_direction=args.oligo_direction, |
| tm=args.tm, |
| output=args.output |
| ) |
| except Exception as e: |
| print(f"Error creating MultiAssemblyDesigner instance: {e}") |
| sys.exit(1) |
|
|
| if __name__ == '__main__': |
| main() |
