48 lines
1.3 KiB
Python
48 lines
1.3 KiB
Python
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# entrypoint.py
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from Bio import SeqIO
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from sqlalchemy.orm import Session
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from app.database import engine, SessionLocal, Base
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from app.models import Sequence, Feature
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import json
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# Tworzenie tabeli w bazie danych
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Base.metadata.create_all(bind=engine)
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def get_db():
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db = SessionLocal()
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try:
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yield db
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finally:
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db.close()
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def load_genbank_to_db(file_path: str):
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db = next(get_db())
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with open(file_path, 'r') as file:
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record = SeqIO.read(file, "genbank")
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# Zapisz sekwencję do bazy danych
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sequence_data = Sequence(
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name=record.name,
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description=record.description,
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sequence=str(record.seq)
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)
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db.add(sequence_data)
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db.commit()
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# Zapisz cechy (features) do bazy danych
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for feature in record.features:
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feature_data = Feature(
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type=feature.type,
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location=str(feature.location),
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sequence=str(record.seq[feature.location.start:feature.location.end]),
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qualifiers=json.dumps(feature.qualifiers),
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sequence_id=sequence_data.id
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)
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db.add(feature_data)
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db.commit()
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print(f"Loaded {file_path} to database.")
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if __name__ == "__main__":
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load_genbank_to_db("data/pET-28+(a).gb")
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