#!/usr/bin/env python3
import sys
from Bio import AlignIO

def convert_fasta_to_phylip(input_file, output_file):
    """
    Конвертирует FASTA файл в формат PHYLIP relaxed
    """
    try:
        with open(input_file, "r") as inh, open(output_file, "w") as outh:
            alignment = AlignIO.parse(inh, "fasta")
            AlignIO.write(alignment, outh, "phylip-relaxed")
        print(f"Успешно сконвертировано {input_file} -> {output_file}")
        return True
    except Exception as e:
        print(f"Ошибка при конвертации: {e}")
        return False

def main():
    if len(sys.argv) != 3:
        print("Использование: python3 fasta_to_phylip.py <input.fasta> <output.phy>")
        print("Пример: python3 fasta_to_phylip.py aligned.fa phr.fa")
        sys.exit(1)
    
    input_file = sys.argv[1]
    output_file = sys.argv[2]
    
    success = convert_fasta_to_phylip(input_file, output_file)
    sys.exit(0 if success else 1)

if __name__ == "__main__":
    main()