outrigger.tests.psi.test_compute module

outrigger.tests.psi.test_compute.dummy_events(splice_type)

outrigger.tests.psi.test_compute.dummy_exons_to_junctions(splice_type, simulated_outrigger_index)

outrigger.tests.psi.test_compute.dummy_isoform1_junction_ids(dummy_isoform1_junction_numbers, dummy_junction_number_to_id)

outrigger.tests.psi.test_compute.dummy_isoform1_junction_numbers(splice_type)

outrigger.tests.psi.test_compute.dummy_isoform1_reads(request, dummy_isoform1_junction_ids)

outrigger.tests.psi.test_compute.dummy_isoform2_junction_ids(dummy_isoform2_junction_numbers, dummy_junction_number_to_id)

outrigger.tests.psi.test_compute.dummy_isoform2_junction_numbers(splice_type)

outrigger.tests.psi.test_compute.dummy_isoform2_reads(request, dummy_isoform2_junction_ids)

outrigger.tests.psi.test_compute.dummy_isoform_junctions(request, dummy_isoform1_junction_numbers, dummy_isoform2_junction_numbers)

outrigger.tests.psi.test_compute.dummy_isoform_reads(dummy_isoform1_reads, dummy_isoform2_reads)

Combine isoform1 and isoform2 reads into one dict

outrigger.tests.psi.test_compute.dummy_junction12()

Junction between exons 1 and 2

outrigger.tests.psi.test_compute.dummy_junction13()

Junction between exons 1 and 3

outrigger.tests.psi.test_compute.dummy_junction14()

Junction between exons 1 and 4

outrigger.tests.psi.test_compute.dummy_junction23()

Junction between exons 2 and 3

outrigger.tests.psi.test_compute.dummy_junction24()

Junction between exons 2 and 4

outrigger.tests.psi.test_compute.dummy_junction34()

Junction between exons 3 and 4

outrigger.tests.psi.test_compute.dummy_junction_locations(dummy_legal_junction_numbers, dummy_junction_number_to_id, incompatible_junctions)

outrigger.tests.psi.test_compute.dummy_junction_number_to_id(dummy_junction12, dummy_junction13, dummy_junction23, dummy_junction14, dummy_junction24, dummy_junction34)

outrigger.tests.psi.test_compute.dummy_legal_junction_numbers(dummy_isoform1_junction_numbers, dummy_isoform2_junction_numbers)

outrigger.tests.psi.test_compute.dummy_splice_junction_reads(dummy_isoform_reads)

Completely fake dataset for sanity checking

outrigger.tests.psi.test_compute.event_annotation(event_annotation_csv)

outrigger.tests.psi.test_compute.event_annotation_csv(splice_type, tasic2016_outrigger_output_index)

outrigger.tests.psi.test_compute.event_df_csv(splice_type, tasic2016_intermediate_psi)

outrigger.tests.psi.test_compute.event_id(splice_type)

outrigger.tests.psi.test_compute.incompatible_junctions(splice_type, dummy_junction14, dummy_junction23)

outrigger.tests.psi.test_compute.isoform1_junctions(splice_type)

outrigger.tests.psi.test_compute.isoform2_junctions(splice_type)

outrigger.tests.psi.test_compute.isoform_read_coverage(request)

outrigger.tests.psi.test_compute.junction_reads_for_rejecting(splice_type, skipped_exon_junction_reads_for_rejecting, mutually_exclusive_exon_junction_reads_for_rejecting)

outrigger.tests.psi.test_compute.mutually_exclusive_exon_junction_reads_for_rejecting(mutually_exclusive_exon_junction_reads_for_rejecting_csv)

outrigger.tests.psi.test_compute.mutually_exclusive_exon_junction_reads_for_rejecting_csv(simulated)

outrigger.tests.psi.test_compute.psi_csv(splice_type, tasic2016_outrigger_output_psi)

outrigger.tests.psi.test_compute.psi_df(psi_csv)

outrigger.tests.psi.test_compute.reads2d(splice_junction_reads_csv)

outrigger.tests.psi.test_compute.single_event_summary_csv(splice_type, tasic2016_intermediate_psi)

outrigger.tests.psi.test_compute.skipped_exon_junction_reads_for_rejecting(skipped_exon_junction_reads_for_rejecting_csv)

outrigger.tests.psi.test_compute.skipped_exon_junction_reads_for_rejecting_csv(simulated)

outrigger.tests.psi.test_compute.splice_junction_reads(splice_junction_reads_csv)

outrigger.tests.psi.test_compute.splice_junction_reads_csv(tasic2016_outrigger_junctions)

outrigger.tests.psi.test_compute.summary_csv(splice_type, tasic2016_outrigger_output_psi)

outrigger.tests.psi.test_compute.summary_df(summary_csv)

outrigger.tests.psi.test_compute.test__check_unequal_read_coverage(isoform_read_coverage)

outrigger.tests.psi.test_compute.test__maybe_parallelize_psi(event_annotation, reads2d, isoform1_junctions, isoform2_junctions, capsys, n_jobs, summary_df)

outrigger.tests.psi.test_compute.test__single_event_psi(event_id, event_df_csv, reads2d, isoform1_junctions, isoform2_junctions, single_event_summary_csv)

outrigger.tests.psi.test_compute.test__single_isoform_maybe_reject(junction_reads_for_rejecting, dummy_isoform1_junction_numbers, dummy_isoform2_junction_numbers)

outrigger.tests.psi.test_compute.test_calculate_psi(event_annotation, reads2d, isoform1_junctions, isoform2_junctions, psi_df, summary_df)