rna_majiq.Events

class rna_majiq.Events(events)

Collections of introns/junctions all starting or ending at the same exon

Parameters:: events (rna_majiq.internals.Events) – Underlying object binding the internal C++ API

__init__(events)

Methods

`__init__`(events)
`broadcast_eidx_to_ecidx`(x[, axis])	Broadcast x over events to event connections
`connection_contig_idx`([ec_idx])	Index into self.contigs for selected event connections
`connection_denovo`([ec_idx])	Indicator if connection was denovo for each selected event connection
`connection_end`([ec_idx])	End coordinate for each selected event connection
`connection_gene_idx`([ec_idx])	Index into self.genes for selected event connections
`connection_other_exon_idx`([ec_idx])	Index into self.exons for nonreference exon for each event connection
`connection_start`([ec_idx])	Start coordinate for each selected event connection
`connections_slice_for_event`(event_idx)	Get slice into event connections for event with specified index
`e_idx_slice_for_gene`(gene_idx)	Get slice into events (e_idx) for specified gene
`ec_dataframe`([annotated, annotated_select])	`pd.DataFrame` over event connections detailing genomic information
`ec_idx_slice_for_event`(e_idx)	Get slice into event connections (ec_idx) for specified event
`event_has_alt_exons`([e_idx])	Indicate if events junctions are connected to more than one other exon
`event_has_other_alt_ss`([e_idx])	Indicate if events junctions use >1 splice sites on a non-reference exon
`event_has_ref_alt_ss`([e_idx])	Indicate if events junctions use >1 splice sites on reference exon
`event_id`([e_idx])	Array of event identifiers for VOILA for specified events
`event_legacy_a3ss`([e_idx])	Indicate if event would be called as a3ss by voila v2
`event_legacy_a5ss`([e_idx])	Indicate if event would be called as a5ss by voila v2
`from_arrays`(introns, junctions, ...)	Create `Events` from connections and input arrays
`from_zarr`(store, introns, junctions)	Load `Events` from specified path/store
`has_intron`([e_idx])	Indicate if selected events have an intron
`index`(ref_exon_idx, event_type)	Get index for specified event in self (-1 if not present)
`merge_dataframes`(df_seq, events_seq[, annotated])	Merge df_seq (index ec_idx, matching events_seq) onto self events
`select_eidx_to_select_ecidx`(select_eidx)	Given index array for e_idx, get index array for associated ec_idx
`slice_for_gene`(gene_idx)	Get slice into events (e_idx) for specified gene
`to_zarr`(store, mode[, consolidated])	Save `Events` to specified path/store
`unique_events_mask`(other)	Get `UniqueEventsMasks` with shared events and events unique to self

Attributes

`connection_e_idx`	Index into events for each event connection
`connection_idx`	Index into self.introns or self.junctions for each event connection
`connection_is_intron`	Indicator if intron/junction for each event connection (alias for is_intron)
`connection_ref_exon_idx`	Index into self.exons for reference exon for each event connection
`contigs`	`Contigs` over which events defined
`df`	`xr.Dataset` with event and event connections information
`df_event_connections`	`xr.Dataset` with event connections information
`df_events`	`xr.Dataset` with event information
`e_idx`	Index over unique events
`e_idx_end`	One-past-end index into events (e_idx) for each gene
`e_idx_start`	First index into events (e_idx) for each gene
`ec_idx`	Index over event connections
`ec_idx_end`	One-past-end index into event connections (ec_idx) for each unique event
`ec_idx_start`	First index into event connections (ec_idx) for each unique event
`event_size`	Number of event connections for each unique event
`event_type`	Indicator if source ('s') or target ('b') for each unique event
`exons`	`Exons` over which events defined
`genes`	`Genes` over which events defined
`introns`	`Introns` over which events defined
`is_intron`	Indicator if an intron or junction for each event connection
`junctions`	`Junctions` over which events defined
`num_connections`	Total number of connections over all events
`num_events`	Number of events
`ref_exon_idx`	Index into self.exons for reference exon of each unique event
`save_df`	`xr.Dataset` that is directly saved for Events