alphagenome.models.dna_output.Output#

class alphagenome.models.dna_output.Output(atac=None, cage=None, dnase=None, rna_seq=None, chip_histone=None, chip_tf=None, splice_sites=None, splice_site_usage=None, splice_junctions=None, contact_maps=None, procap=None)[source]#

Model outputs for a single prediction.

atac#

TrackData of type OutputType.ATAC.

cage#

TrackData of type OutputType.CAGE.

dnase#

TrackData of type OutputType.DNASE.

rna_seq#

TrackData of type OutputType.RNA_SEQ.

chip_histone#

TrackData of type OutputType.CHIP_HISTONE.

chip_tf#

TrackData of type OutputType.CHIP_TF.

splice_sites#

TrackData of type OutputType.SPLICE_SITES.

splice_site_usage#

TrackData of type OutputType.SPLICE_SITE_USAGE.

splice_junctions#

TrackData of type OutputType.SPLICE_JUNCTIONS.

contact_maps#

TrackData of type OutputType.CONTACT_MAPS.

procap#

TrackData of type OutputType.PROCAP.

Attributes#

Table

Output.atac: TrackData | None = None#
Output.cage: TrackData | None = None#
Output.chip_histone: TrackData | None = None#
Output.chip_tf: TrackData | None = None#
Output.contact_maps: TrackData | None = None#
Output.dnase: TrackData | None = None#
Output.procap: TrackData | None = None#
Output.rna_seq: TrackData | None = None#
Output.splice_junctions: JunctionData | None = None#
Output.splice_site_usage: TrackData | None = None#
Output.splice_sites: TrackData | None = None#

Methods#

Table

filter_ontology_terms(ontology_terms)

Filters tracks to specific ontology terms.

filter_output_type(output_types)

Filters tracks to specific output type.

filter_to_strand(strand)

Filters tracks by DNA strand.

get(output_type)

Gets the track data for the specified output type.

map_track_data(fn)

Applies a transformation function to each TrackData.

resize(width)

Resizes all track data to a specified width.

Output.filter_ontology_terms(ontology_terms)[source]#

Filters tracks to specific ontology terms.

Parameters:

ontology_terms (Iterable[OntologyTerm]) – An iterable of OntologyTerm objects to filter to.

Return type:

Output

Returns:

A new Output object with only the tracks associated with the specified ontology terms.

Output.filter_output_type(output_types)[source]#

Filters tracks to specific output type.

Parameters:

output_types (Iterable[OutputType]) – An iterable of OutputType enums to filter by.

Return type:

Output

Returns:

A new Output object with only the tracks of the specified output types.

Output.filter_to_strand(strand)[source]#

Filters tracks by DNA strand.

Parameters:

strand (Literal['+', '-', '.']) – The strand to filter by (‘+’, ‘-’, or ‘.’).

Return type:

Output

Returns:

A new Output object with only the tracks on the specified strand.

Output.get(output_type)[source]#

Gets the track data for the specified output type.

Parameters:

output_type (OutputType) – The type of output to retrieve.

Return type:

TrackData | JunctionData | None

Returns:

The track data for the specified output type, or None if no such data exists.

Output.map_track_data(fn)[source]#

Applies a transformation function to each TrackData.

Parameters:

fn (Callable[[TrackData, OutputType], TrackData | None]) – The function to apply to each TrackData. It should take a TrackData object and an OutputType enum as input and return a TrackData object or None.

Return type:

Output

Returns:

A new Output object with the transformed track data.

Output.resize(width)[source]#

Resizes all track data to a specified width.

Parameters:

width (int) – The desired width in base pairs.

Return type:

Output

Returns:

A new Output object with resized track data.