cogent3.core.annotation_db.BasicAnnotationDb#

class BasicAnnotationDb(*args, **kwargs)#

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

Notes

This is the default db on Sequence, SequenceCollection and Alignment

Attributes
db
describe

top level description of the annotation db

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

compatible(other_db[, symmetric])

checks whether table_names are compatible

count_distinct(*[, seqid, biotype, name])

return table of counts of distinct values

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

num_matches(*[, seqid, biotype, name, ...])

return the number of records matching condition

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

StrOrBool

add_records

from_dict

get_features_matching

to_json