outrigger.tests.index.test_events module

class outrigger.tests.index.test_events.TestEventMaker

Bases: object

Methods

event_maker(junction_exon_triples)
events_csv(simulated_outrigger_index, ...)
strand_name(strand)
test_a3ss(event_maker, strand)
test_a5ss(event_maker, strand)
test_afe(event_maker, strand)
test_ale(event_maker, strand)
test_finding_events(event_maker, capsys, ...)	Test finding SE and MXE events in one function
test_init(junction_exon_triples)

event_maker(junction_exon_triples)

events_csv(simulated_outrigger_index, strand_name)

strand_name(strand)

test_a3ss(event_maker, strand)

test_a5ss(event_maker, strand)

test_afe(event_maker, strand)

test_ale(event_maker, strand)

test_finding_events(event_maker, capsys, strand_name, splice_type, simulated_outrigger_index)

Test finding SE and MXE events in one function

test_init(junction_exon_triples)

class outrigger.tests.index.test_events.TestSpliceGraph

Bases: object

Methods

exon1_i(strand)
exon1_name(splice_graph, exon1_i)
mutually_exclusive_events(strand)
skipped_exon_events(strand)
splice_graph(junction_exon_triples)
test___init__(junction_exon_triples, graph_items)
test__mutually_exclusive_exon(splice_graph, ...)
test__skipped_exon(splice_graph, exon1_i, ...)
test_exons_one_junction_upstream(...)
test_exons_two_junctions_downstream(...)
test_junctions_between_exons(splice_graph, ...)
test_single_exon_alternative_events(...)

exon1_i(strand)

exon1_name(splice_graph, exon1_i)

mutually_exclusive_events(strand)

skipped_exon_events(strand)

splice_graph(junction_exon_triples)

test___init__(junction_exon_triples, graph_items)

test__mutually_exclusive_exon(splice_graph, exon1_i, exon1_name, mutually_exclusive_events)

test__skipped_exon(splice_graph, exon1_i, exon1_name, skipped_exon_events)

test_exons_one_junction_upstream(splice_graph, exon1_i, strand)

test_exons_two_junctions_downstream(splice_graph, exon1_i, strand)

test_junctions_between_exons(splice_graph, strand, exon1_i)

test_single_exon_alternative_events(splice_graph, exon1_i, exon1_name, mutually_exclusive_events, skipped_exon_events)

outrigger.tests.index.test_events.assert_graph_items_equal(graph1, items1, graph2, items2)

Checks all relationships in graph1 exist in graph2, and vice versa

outrigger.tests.index.test_events.chrom()

outrigger.tests.index.test_events.exon_start_stop()

outrigger.tests.index.test_events.graph_items(exon_start_stop, transcripts, chrom, strand)

outrigger.tests.index.test_events.junction_exon_triples(chrom, exon_start_stop, transcripts, strand)

outrigger.tests.index.test_events.junction_to_exons(chrom, exon_start_stop, transcripts, strand)

outrigger.tests.index.test_events.region(request)

outrigger.tests.index.test_events.test_stringify_location(chrom, strand, region)

outrigger.tests.index.test_events.transcripts()