inf04-web2/entrypoint.py

from Bio import SeqIO
from sqlalchemy.orm import Session
from app.database import engine, SessionLocal, Base
from app.models import Sequence, Feature
import json

# Tworzenie tabeli w bazie danych
Base.metadata.create_all(bind=engine)

def get_db():
    db = SessionLocal()
    try:
        yield db
    finally:
        db.close()

def load_genbank_to_db(file_path: str):
    db = next(get_db())
    with open(file_path, 'r') as file:
        record = SeqIO.read(file, "genbank")

        # Zapisz sekwencję do bazy danych
        sequence_data = Sequence(
            name=record.name,
            description=record.description if 'description' in record.annotations else 'No description',
            sequence=str(record.seq)
        )
        db.add(sequence_data)
        db.commit()
        db.refresh(sequence_data)  # Odśwież sekwencję, aby uzyskać jej ID

        # Zapisz cechy (features) do bazy danych
        for feature in record.features:
            if feature.type in ["promoter", "RBS","CDS", "protein_bind", "misc_feature", "rep_origin", "terminator"]:
                qualifiers = {}
                if feature.type == "CDS":
                    qualifiers['gene_name'] = feature.qualifiers.get('gene', ['Unknown gene'])[0]
                    qualifiers['product'] = feature.qualifiers.get('product', ['Unknown product'])[0]
                elif feature.type == "protein_bind":
                    qualifiers['binding_site'] = feature.qualifiers.get('bound_moiety', ['Unknown binding site'])[0]
                elif feature.type == "misc_feature":
                    qualifiers['note'] = feature.qualifiers.get('note', ['No additional information'])[0]
                elif feature.type == "rep_origin":
                    qualifiers['note'] = "This is a replication origin."
                
                feature_data = Feature(
                    type=feature.type,
                    location=str(feature.location),
                    sequence=str(record.seq[feature.location.start:feature.location.end]),
                    qualifiers=json.dumps(qualifiers),
                    sequence_id=sequence_data.id  # Ustawienie poprawnego ID
                )
                db.add(feature_data)
        db.commit()
    print(f"Loaded {file_path} to database.")

if __name__ == "__main__":
    load_genbank_to_db("data/plasmid.gb")