thapbi_pict.db_orm module
Object Relational Mapping for marker sequence database.
Using SQLalchemy, the Python classes defined here give us a database schema and the code to import/export the data as Python objects.
- class thapbi_pict.db_orm.Base(*args: Any, **kwargs: Any)
Bases:
DeclarativeBase
Base class for SQLAlchemy ORM declarations.
See the SQLAlchemy 2.0 documentation. This is expected to be compatible with type checkers like mypy.
- class thapbi_pict.db_orm.DataSource(*args: Any, **kwargs: Any)
Bases:
Base
Database entry for a data source (NCBI, curated, etc).
Each accession is expected to be unique within a data source.
- class thapbi_pict.db_orm.MarkerDef(*args: Any, **kwargs: Any)
Bases:
Base
Database entry for a marker listing primers and amplicon length limits.
- class thapbi_pict.db_orm.MarkerSeq(*args: Any, **kwargs: Any)
Bases:
Base
Database entry for a single marker reference sequence.
- class thapbi_pict.db_orm.SeqSource(*args: Any, **kwargs: Any)
Bases:
Base
Database entry for source of a marker sequence entry.
- source
alias of
DataSource
- class thapbi_pict.db_orm.Synonym(*args: Any, **kwargs: Any)
Bases:
Base
Database entry for a synonym of a taxonomy entry.
In addition to direct synonyms, includes the names and synonyms of any child nodes of the species (e.g. variants, strains, etc).
- class thapbi_pict.db_orm.Taxonomy(*args: Any, **kwargs: Any)
Bases:
Base
Database entry for a species’ taxonomy entry.
- thapbi_pict.db_orm.connect_to_db(*args, **kwargs)
Create engine and return session bound to it.
>>> Session = connect_to_db("sqlite:///:memory:", echo=True) >>> session = Session()