outrigger.index.events module

class outrigger.index.events.EventMaker(junction_exon_triples, db=None, junction_col='junction', exon_col='exon')

Bases: object

Combine splice junctions into splicing events

Parameters:

junction_exon_triples : pandas.DataFrame

of “exon, direction, junction”, e.g.: exon1, upstream, junction12

db : gffutils.FeatureDB

Gffutils Database of gene, transcript, and exon features. The exons must be accessible by the id provided on the exon_col columns. If not provided, certain splice types which require information about the transcript (AFE, ALE) cannot be annotated.

Attributes

exon_progress_interval

Methods

add_event_id_col(events, splice_type)
add_incompatible_junctions(events, splice_type)	Add junctions that are incompatible with splice type definition
event_dict_to_df(events, exon_names, ...)
find_events([splice_types, n_jobs])	For each exon, test if it is part of an alternative event

add_event_id_col(events, splice_type)

add_incompatible_junctions(events, splice_type)

Add junctions that are incompatible with splice type definition

event_dict_to_df(events, exon_names, junction_names)

exon_progress_interval

find_events(splice_types=('se', 'mxe'), n_jobs=-1)

For each exon, test if it is part of an alternative event

class outrigger.index.events.SpliceGraph(junction_exon_triples, junction_col='junction', exon_col='exon', splice_types=('se', 'mxe'))

Bases: object

Methods

alternative_events()
exons_one_junction_downstream(exon_i)	Get the exon(s) that are immediately downstream of this one
exons_one_junction_upstream(exon_query)	Get the exon(s) that are immediately upstream of this one
exons_two_junctions_downstream(exon_i)	Get the exon(s) that are two junction hops downstream
junctions_between_exons(exon_a, exon_b)	Get the junctions between exonA and exonB
single_exon_alternative_events(exon_i, exon_name)

alternative_events()

exons_one_junction_downstream(exon_i)

Get the exon(s) that are immediately downstream of this one

Get exons that are downstream from this one, separated by one junction

Parameters:

exon_i : int

Integer identifier of the exon whose downstream exons you want. This is the exon’s index location in self.exon_cols

Returns:

downstream_exons : graphlite.Query

Integer identfiers of exons which are one junction downstream of the provided one

exons_one_junction_upstream(exon_query)

Get the exon(s) that are immediately upstream of this one

Get exons that are upstream from this one, separated by one junction

Parameters:

exon_query : graphlite.Query

Integer identifier of the exon whose upstream exons you want. This is the exon’s index location in self.exons

Returns:

upstream_exons : graphlite.Query

Integer identfiers of exon_cols which are one junction upstream of the provided one

exons_two_junctions_downstream(exon_i)

Get the exon(s) that are two junction hops downstream

Go one exon downstream, then one more exon. This is all the 2nd level exon_cols

Parameters:

exon_i : int

Integer identifier of the exon whose downstream exon_cols you want. This is the exon’s index location in self.exon_cols

Returns:

downstream_exons : graphlite.Query

Integer identfiers of exon_cols which are separated from the original exon by a junction, exon, and another junction

junctions_between_exons(exon_a, exon_b)

Get the junctions between exonA and exonB

single_exon_alternative_events(exon_i, exon_name)

outrigger.index.events.make_splice_graph_find_events(df, junction_col, exon_col, splice_types=('se', 'mxe'))

outrigger.index.events.opposite(direction)

outrigger.index.events.stringify_location(chrom, start, stop, strand, region=None)

Convert genome location to a string, optionally prefixing with region