BioSQL.BioSeq module

Implementations of Biopython-like Seq objects on top of BioSQL.

This allows retrieval of items stored in a BioSQL database using a biopython-like SeqRecord and Seq interface.

Note: Currently we do not support recording per-letter-annotations (like quality scores) in BioSQL.

class BioSQL.BioSeq.DBSeqRecord(adaptor, primary_id)

Bases: SeqRecord

BioSQL equivalent of the Biopython SeqRecord object.

__init__(adaptor, primary_id)

Create a DBSeqRecord object.

Arguments:

• adaptor - A BioSQL.BioSeqDatabase.Adaptor object

• primary_id - An internal integer ID used by BioSQL

You wouldn’t normally create a DBSeqRecord object yourself, this is done for you when using a BioSeqDatabase object

property seq

Seq object

property dbxrefs: list[str]

Database cross references.

property features

Features

property annotations: dict[str, str | int]

Annotations.