outrigger.io.gtf module

Functions for creating GTF databases using gffutils and using those databases to annotate alternative events.

class outrigger.io.gtf.SplicingAnnotator(db, events, splice_type)

Bases: object

Annotates basic features of splicing events: gene ids and names

Methods

attributes()	Retrieve all GTF attributes for each isoform’s event
event_introns_regions(exons)	Make intron and event regions for an event
exon_bedfiles(folder)
maybe_get_feature(feature_id)

Annotate splicing events with their respective genes

Parameters:

db : gffutils.FeatureDB

Database including all the exons found in the events

events : pandas.DataFrame

Table of events, with the event ids as the index

splice_type : ‘se’ | ‘mxe’

The type of alternative splicing, which informs the exon configurations for different isoforms

Methods

attributes()	Retrieve all GTF attributes for each isoform’s event
event_introns_regions(exons)	Make intron and event regions for an event
exon_bedfiles(folder)
maybe_get_feature(feature_id)

attributes()

Retrieve all GTF attributes for each isoform’s event

event_introns_regions(exons)

Make intron and event regions for an event

Parameters:

exons : outrigger.Regions

List of exon ids, e.g. [“exon:chr1:100-200:+”, “exon:chr1:300-400:+”]

Returns:

regions : dict

exon_bedfiles(folder)

maybe_get_feature(feature_id)

outrigger.io.gtf.create_db(gtf_filename, db_filename=None)

outrigger.io.gtf.location_to_feature(db, chrom, start, stop, strand, source, featuretype)

outrigger.io.gtf.maybe_analyze(db)

outrigger.io.gtf.transform(f)