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sequences and api are ok

This commit is contained in:
mpabi 2024-06-20 20:19:38 +00:00
parent e790db7bb7
commit 68367f04c3
2 changed files with 24 additions and 15 deletions
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3
app/models.py
View File

@ -1,7 +1,6 @@
# app/models.py
from sqlalchemy import Column, Integer, String, Text, ForeignKey from sqlalchemy import Column, Integer, String, Text, ForeignKey
from sqlalchemy.orm import relationship from sqlalchemy.orm import relationship
from .database import Base from app.database import Base
class Sequence(Base): class Sequence(Base):
__tablename__ = "sequences" __tablename__ = "sequences"

36
entrypoint.py
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@ -1,5 +1,3 @@
#%%
# entrypoint.py
from Bio import SeqIO from Bio import SeqIO
from sqlalchemy.orm import Session from sqlalchemy.orm import Session
from app.database import engine, SessionLocal, Base from app.database import engine, SessionLocal, Base
@ -9,7 +7,6 @@ import json
# Tworzenie tabeli w bazie danych # Tworzenie tabeli w bazie danych
Base.metadata.create_all(bind=engine) Base.metadata.create_all(bind=engine)
#%%
def get_db(): def get_db():
db = SessionLocal() db = SessionLocal()
try: try:
@ -25,25 +22,38 @@ def load_genbank_to_db(file_path: str):
# Zapisz sekwencję do bazy danych # Zapisz sekwencję do bazy danych
sequence_data = Sequence( sequence_data = Sequence(
name=record.name, name=record.name,
description=record.description, description=record.description if 'description' in record.annotations else 'No description',
sequence=str(record.seq) sequence=str(record.seq)
) )
db.add(sequence_data) db.add(sequence_data)
db.commit() db.commit()
db.refresh(sequence_data) # Odśwież sekwencję, aby uzyskać jej ID
# Zapisz cechy (features) do bazy danych # Zapisz cechy (features) do bazy danych
for feature in record.features: for feature in record.features:
feature_data = Feature( if feature.type in ["promoter", "RBS","CDS", "protein_bind", "misc_feature", "rep_origin", "terminator"]:
type=feature.type, qualifiers = {}
location=str(feature.location), if feature.type == "CDS":
sequence=str(record.seq[feature.location.start:feature.location.end]), qualifiers['gene_name'] = feature.qualifiers.get('gene', ['Unknown gene'])[0]
qualifiers=json.dumps(feature.qualifiers), qualifiers['product'] = feature.qualifiers.get('product', ['Unknown product'])[0]
sequence_id=sequence_data.id elif feature.type == "protein_bind":
) qualifiers['binding_site'] = feature.qualifiers.get('bound_moiety', ['Unknown binding site'])[0]
db.add(feature_data) 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() db.commit()
print(f"Loaded {file_path} to database.") print(f"Loaded {file_path} to database.")
if __name__ == "__main__": if __name__ == "__main__":
load_genbank_to_db("data/pET-28+(a).gb") load_genbank_to_db("data/plasmid.gb")