cogent3.core.annotation_db.BasicAnnotationDb

class BasicAnnotationDb(*args: Any, **kwargs: Any)

Provides a user table for annotations. This can be merged with either the Gff or Genbank versions.

Attributes:

db

describe

top level description of the annotation db

schema_version

Return the schema version of this database.

table_names

Methods

add_feature(*, seqid, biotype, name, spans)	adds a record to user table
biotype_counts()	return counts of biological types across all tables and seqids
close()	closes the db
compatible(other_db[, symmetric])	checks whether table_names are compatible
count_distinct(*[, seqid, biotype, name])	return table of counts of distinct values
from_file(path)	Load an annotation database from a file.
get_feature_children(name[, biotype])	yields children of name
get_feature_parent(name, **kwargs)	yields parents of name
get_records_matching(*[, biotype, seqid, ...])	return all fields for matching records
make_indexes()	adds db indexes for core attributes
num_matches(*[, seqid, biotype, name, ...])	return the number of records matching condition
subset(*[, source, biotype, seqid, name, ...])	returns a new db instance with records matching the provided conditions
to_rich_dict()	returns a dict suitable for json serialisation
union(annot_db)	returns a new instance with merged records with other
update(annot_db[, seqids])	update records with those from an instance of the same type
write(path)	writes db as bytes to path

add_records
from_dict
get_features_matching
to_json

Notes

This is the default db on Sequence, SequenceCollection and Alignment