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genomic_features.ensembl.EnsemblDB

genomic_features.ensembl.EnsemblDB#

class genomic_features.ensembl.EnsemblDB(connection)#

Ensembl annotation database.

Attributes table#

metadata

Metadata for the database as a dict (e.g. who built it, when, with what resource).

Methods table#

chromosomes()

Get chromosome information (seq_name, length, etc.).

exons([cols, filter, join_type])

Get exons table.

genes([cols, filter, join_type])

Get gene annotations.

list_columns([tables])

List queryable columns available in these tables.

list_tables()

List all tables available in the genomic features database.

transcripts([cols, filter, join_type])

Get transcript annotations.

Attributes#

EnsemblDB.metadata#

Metadata for the database as a dict (e.g. who built it, when, with what resource).

Methods#

EnsemblDB.chromosomes()#

Get chromosome information (seq_name, length, etc.).

Return type:

DataFrame

Usage#

>>> ensdb.chromosomes()
EnsemblDB.exons(cols=None, filter=EmptyFilter(), join_type='inner')#

Get exons table.

Parameters:

  • cols (Optional[list[str]] (default: None)) – Which columns to retrieve from the database. Can be from other tables. Returns all exon columns if None.

  • filter (AbstractFilterExpr (default: EmptyFilter())) – Filter to apply to the query.

  • join_type (Literal['inner', 'left'] (default: 'inner')) – Type of join to use for the query.

Return type:

DataFrame

Usage#

>>> ensdb.exons()
EnsemblDB.genes(cols=None, filter=EmptyFilter(), join_type='inner')#

Get gene annotations.

Parameters:

  • cols (Optional[list[str]] (default: None)) – Which columns to retrieve from the database. Can be from other tables. Returns all gene columns if None.

  • filters – Filters to apply to the query.

  • join_type (Literal['inner', 'left'] (default: 'inner')) – How to perform joins during the query (if cols or filters requires them).

Return type:

DataFrame

Usage#

>>> ensdb.genes(cols=["gene_id", "gene_name", "tx_id"])
EnsemblDB.list_columns(tables=None)#

List queryable columns available in these tables.

Return type:

list[str]

EnsemblDB.list_tables()#

List all tables available in the genomic features database.

Return type:

list

EnsemblDB.transcripts(cols=None, filter=EmptyFilter(), join_type='inner')#

Get transcript annotations.

Parameters:

  • cols (Optional[list[str]] (default: None)) – Which columns to retrieve from the database. Can be from other tables. Returns all transcript columns if None.

  • filters – Filters to apply to the query.

  • join_type (Literal['inner', 'left'] (default: 'inner')) – How to perform joins during the query (if cols or filters requires them).

Return type:

DataFrame

Usage#

>>> ensdb.transcripts(cols=["tx_id", "tx_name", "gene_id"])
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