GenbankAnnotationDb#

class GenbankAnnotationDb(*args, **kwargs)#

Support for annotations from Genbank files.

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
`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
`get_feature_children`(name[, biotype, ...])	yields children of name
`get_feature_parent`(name[, exclude_biotype, ...])	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

StrOrBool
add_records
from_dict
get_features_matching
to_json

Notes

Extended attributes are stored as json in the gb, attributes column.

StrOrBool#: alias of str | bool

add_feature(*, seqid: str, biotype: str, name: str, spans: List[Tuple[int, int]], parent_id: str | None = None, strand: str | None = None, attributes: str | None = None, on_alignment: bool | None = False) → None#

adds a record to user table

Parameters:

seqidstr: name of the sequence feature resides on
biotypestr: biological type of the record
namestr: the name of a record, an identifier
spanstyping.List[typing.Tuple[int, int]], optional: this will be sorted
strandstr, optional: either +, -. Defaults to ‘+’
attributesstr, optional: additional attributes as a string
on_alignmentbool, optional: whether the annotation is an alignment annotation

add_records(records, seqid)#

biotype_counts() → dict#: return counts of biological types across all tables and seqids

close()#: closes the db

compatible(other_db: SupportsFeatures, symmetric=True) → bool#

checks whether table_names are compatible

Parameters:

other_db: the other annotation db instance
symmetric: checks only that tables of other_db equal, or are a subset, of mine

count_distinct(*, seqid: StrOrBool = False, biotype: StrOrBool = False, name: StrOrBool = False) → Optional[Table]#

return table of counts of distinct values

Parameters:

seqid, biotype, name: if a string, selects the subset of rows matching the provided values and counts distinct values for the other fields whose value is True.

Returns:

Table with columns corresponding to argument whose value was True

Examples

To compute copy number by gene name within each genome

>>> counts_table = db.count_distinct(seqid=True, biotype="gene", name=True)

property db: Connection#

property describe: Table#: top level description of the annotation db

classmethod from_dict(data: dict)#

get_feature_children(name: str, biotype: str | None = None, exclude_biotype: str | None = None, start: int | None = None, stop: int | None = None) → Iterator[FeatureDataType]#: yields children of name

get_feature_parent(name: str, exclude_biotype: str | None = None, start: int | None = None, stop: int | None = None) → Iterator[FeatureDataType]#: yields parents of name

get_features_matching(*, biotype: str = None, seqid: str = None, name: str = None, start: int = None, stop: int = None, strand: str | None = None, attributes: str | None = None, on_alignment: bool = None, allow_partial: bool = False) → Iterator[FeatureDataType]#

get_records_matching(*, biotype: str = None, seqid: str = None, name: str = None, start: int = None, stop: int = None, strand: str | None = None, attributes: str | None = None, on_alignment: bool = None, allow_partial: bool = False) → Iterator[dict]#: return all fields for matching records

make_indexes()#: adds db indexes for core attributes

num_matches(*, seqid: str | None = None, biotype: str | None = None, name: str | None = None, strand: str | None = None, attributes: str | None = None, on_alignment: bool | None = None) → int#: return the number of records matching condition

subset(*, source: str | PathLike | PurePath = ':memory:', biotype: str = None, seqid: str = None, name: str = None, start: int | None = None, stop: int | None = None, strand: str | None = None, attributes: str | None = None, allow_partial: bool = False) → Self#: returns a new db instance with records matching the provided conditions

property table_names: tuple[str]#

to_json() → str#

to_rich_dict() → dict#: returns a dict suitable for json serialisation

union(annot_db: SupportsFeatures) → SupportsFeatures#

returns a new instance with merged records with other

Parameters:

annot_db: an annotation db whose schema is either a subset, or superset of self

Returns:

The class whose schema contains the other

update(annot_db: SupportsFeatures, seqids: str | List[str] | None = None) → None#: update records with those from an instance of the same type

write(path: str | PathLike | PurePath) → None#: writes db as bytes to path