cogent3.core.annotation_db.GffAnnotationDb#

class GffAnnotationDb(*args: Any, **kwargs: Any)#

Support for annotations from gff files. Records that span multiple rows in the gff are merged into a single record.

Attributes:

Methods

`add_feature`(*, seqid, biotype, name, spans)	adds a record to user table
`add_records`(reduced, **kwargs)
`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
`update_record_spans`(*, name, spans)	updates spans attribute of a gff table record if present
`write`(path)	writes db as bytes to path