Index

A

add_event_id_col() (outrigger.index.events.EventMaker method) add_exons_and_junction_ids() (in module outrigger.io.core) add_incompatible_junctions() (outrigger.index.events.EventMaker method) adjacencies() (outrigger.tests.index.test_adjacencies.TestExonJunctionAdjacencies method) adjacent_in_genome() (outrigger.tests.index.test_adjacencies.TestExonJunctionAdjacencies method) adjacent_in_genome_downstream() (outrigger.tests.index.test_adjacencies.TestExonJunctionAdjacencies method)

adjacent_in_genome_template() (outrigger.tests.index.test_adjacencies.TestExonJunctionAdjacencies method) adjacent_in_genome_upstream() (outrigger.tests.index.test_adjacencies.TestExonJunctionAdjacencies method) alternative_events() (outrigger.index.events.SpliceGraph method) assert_directories_equal() (in module outrigger.tests.test_commandline) assert_graph_items_equal() (in module outrigger.tests.index.test_events) attributes() (outrigger.io.gtf.SplicingAnnotator method)

B

bam_filenames() (in module outrigger.tests.conftest)

bam_to_junction_reads_table() (in module outrigger.io.bam) bamfile() (in module outrigger.tests.io.test_bam)

C

calculate_psi() (in module outrigger.psi.compute) chrom (outrigger.region.Region attribute) chrom() (in module outrigger.tests.index.test_events)

CommandLine (class in outrigger.commandline) create_db() (in module outrigger.io.gtf) csv() (outrigger.commandline.Subcommand method)

D

data_folder() (in module outrigger.tests.conftest) db() (in module outrigger.tests.conftest) db_filename() (in module outrigger.tests.conftest) debug (outrigger.commandline.Subcommand attribute) detect_exons_from_junctions() (outrigger.index.adjacencies.ExonJunctionAdjacencies method) direction() (in module outrigger.tests.validate.test_check_splice_sites) do_not_have_mysql() (in module outrigger.tests.validate.test_check_splice_sites) do_usage_and_die() (outrigger.commandline.CommandLine method) done() (in module outrigger.util) dummy_events() (in module outrigger.tests.psi.test_compute) dummy_exons_to_junctions() (in module outrigger.tests.psi.test_compute) dummy_isoform1_junction_ids() (in module outrigger.tests.psi.test_compute) dummy_isoform1_junction_numbers() (in module outrigger.tests.psi.test_compute) dummy_isoform1_reads() (in module outrigger.tests.psi.test_compute)

dummy_isoform2_junction_ids() (in module outrigger.tests.psi.test_compute) dummy_isoform2_junction_numbers() (in module outrigger.tests.psi.test_compute) dummy_isoform2_reads() (in module outrigger.tests.psi.test_compute) dummy_isoform_junctions() (in module outrigger.tests.psi.test_compute) dummy_isoform_reads() (in module outrigger.tests.psi.test_compute) dummy_junction12() (in module outrigger.tests.psi.test_compute) dummy_junction13() (in module outrigger.tests.psi.test_compute) dummy_junction14() (in module outrigger.tests.psi.test_compute) dummy_junction23() (in module outrigger.tests.psi.test_compute) dummy_junction24() (in module outrigger.tests.psi.test_compute) dummy_junction34() (in module outrigger.tests.psi.test_compute) dummy_junction_locations() (in module outrigger.tests.psi.test_compute) dummy_junction_number_to_id() (in module outrigger.tests.psi.test_compute) dummy_legal_junction_numbers() (in module outrigger.tests.psi.test_compute) dummy_splice_junction_reads() (in module outrigger.tests.psi.test_compute)

E

empty() (in module outrigger.tests.io.test_bam) event_annotation() (in module outrigger.tests.psi.test_compute) event_annotation_csv() (in module outrigger.tests.psi.test_compute) event_df_csv() (in module outrigger.tests.psi.test_compute) event_dict_to_df() (outrigger.index.events.EventMaker method) event_id() (in module outrigger.tests.psi.test_compute) event_introns_regions() (outrigger.io.gtf.SplicingAnnotator method) event_maker() (outrigger.tests.index.test_events.TestEventMaker method) EventMaker (class in outrigger.index.events) events_csv() (outrigger.tests.index.test_events.TestEventMaker method) execute() (outrigger.commandline.Index method) (outrigger.commandline.Psi method) (outrigger.commandline.Validate method)

exon1_i() (outrigger.tests.index.test_events.TestSpliceGraph method) exon1_name() (outrigger.tests.index.test_events.TestSpliceGraph method) exon2_bed() (in module outrigger.tests.validate.test_check_splice_sites) exon_bedfiles() (outrigger.io.gtf.SplicingAnnotator method) exon_pair_splice_sites() (outrigger.commandline.Validate method) exon_progress_interval (outrigger.index.events.EventMaker attribute) exon_start_stop() (in module outrigger.tests.index.test_events) exon_types (outrigger.index.adjacencies.ExonJunctionAdjacencies attribute) ExonJunctionAdjacencies (class in outrigger.index.adjacencies) exons_one_junction_downstream() (outrigger.index.events.SpliceGraph method) exons_one_junction_upstream() (outrigger.index.events.SpliceGraph method) exons_two_junctions_downstream() (outrigger.index.events.SpliceGraph method) extract_alternative_constitutive() (in module outrigger.util)

F

filter_junctions_on_reads() (outrigger.commandline.Subcommand method) find_events() (outrigger.index.events.EventMaker method) folders (outrigger.commandline.Psi attribute) (outrigger.commandline.Subcommand attribute) (outrigger.commandline.SubcommandAfterIndex attribute)

force (outrigger.commandline.Subcommand attribute)

G

genome_name() (in module outrigger.tests.validate.test_check_splice_sites) get_event_attributes() (outrigger.commandline.Index method) gffutils_db (outrigger.commandline.Subcommand attribute)

graph_items() (in module outrigger.tests.index.test_events) gtf_filename (outrigger.commandline.Subcommand attribute) gtf_filename() (in module outrigger.tests.conftest) gtf_folder (outrigger.commandline.Subcommand attribute)

I

ignore_multimapping (outrigger.commandline.Subcommand attribute) ignore_multimapping() (in module outrigger.tests.conftest) incompatible_junctions() (in module outrigger.tests.psi.test_compute) Index (class in outrigger.commandline) index() (outrigger.commandline.CommandLine method) index_folder (outrigger.commandline.Subcommand attribute)

individual_exon_splice_sites() (outrigger.commandline.Validate method) input_index (outrigger.commandline.SubcommandAfterIndex attribute) int_to_junction_motif() (in module outrigger.io.star) is_there_an_exon_here() (in module outrigger.index.adjacencies) isoform1_junctions() (in module outrigger.tests.psi.test_compute) isoform2_junctions() (in module outrigger.tests.psi.test_compute) isoform_read_coverage() (in module outrigger.tests.psi.test_compute)

J

junction_exon_triples() (in module outrigger.tests.index.test_events) junction_id_col (outrigger.commandline.Psi attribute) junction_metadata() (in module outrigger.tests.conftest) (outrigger.commandline.Subcommand static method) junction_reads() (in module outrigger.tests.conftest)

junction_reads_filename (outrigger.commandline.Subcommand attribute) junction_reads_for_rejecting() (in module outrigger.tests.psi.test_compute) junction_to_exons() (in module outrigger.tests.index.test_events) junctions_adjacent_to_this_exon() (outrigger.index.adjacencies.ExonJunctionAdjacencies method) junctions_between_exons() (outrigger.index.events.SpliceGraph method) junctions_folder (outrigger.commandline.Subcommand attribute)

L

location() (in module outrigger.tests.index.test_region)

location_to_feature() (in module outrigger.io.gtf) location_with_region_name() (in module outrigger.tests.index.test_region)

M

main() (in module outrigger.commandline) make_events_by_traversing_graph() (outrigger.commandline.Index method) make_exon_junction_adjacencies() (outrigger.commandline.Index method) make_graph() (outrigger.commandline.Index static method) make_junction_reads_file() (outrigger.commandline.Subcommand method) make_metadata() (in module outrigger.io.star) make_splice_graph_find_events() (in module outrigger.index.events) max_de_novo_exon_length (outrigger.commandline.Index attribute) maybe_analyze() (in module outrigger.io.gtf) maybe_chromsizes() (in module outrigger.tests.validate.test_check_splice_sites) maybe_get_feature() (outrigger.io.gtf.SplicingAnnotator method) maybe_get_validated_events() (outrigger.commandline.Psi method)

maybe_make_db() (outrigger.commandline.Subcommand method) maybe_make_folder() (outrigger.commandline.Subcommand method) maybe_overwrite() (outrigger.commandline.Subcommand method) maybe_read_chromsizes() (in module outrigger.validate.check_splice_sites) maybe_read_junction_reads() (outrigger.commandline.Psi method) min_reads (outrigger.commandline.Subcommand attribute) multi() (in module outrigger.tests.io.test_bam) multi_csv() (in module outrigger.tests.io.test_bam) multiple_bams_reads_table_csvs() (in module outrigger.tests.io.test_bam) mutually_exclusive_events() (outrigger.tests.index.test_events.TestSpliceGraph method) mutually_exclusive_exon_junction_reads_for_rejecting() (in module outrigger.tests.psi.test_compute) mutually_exclusive_exon_junction_reads_for_rejecting_csv() (in module outrigger.tests.psi.test_compute) myl6_novel_exon_junction() (in module outrigger.tests.conftest)

N

n_jobs() (in module outrigger.tests.conftest) name (outrigger.region.Region attribute)

negative_control_folder() (in module outrigger.tests.conftest) negative_control_output() (in module outrigger.tests.conftest)

O

opposite() (in module outrigger.index.events) output_folder (outrigger.commandline.Subcommand attribute) outrigger (module) outrigger.commandline (module) outrigger.common (module) outrigger.index (module) outrigger.index.adjacencies (module) outrigger.index.events (module) outrigger.io (module) outrigger.io.bam (module) outrigger.io.core (module) outrigger.io.gtf (module) outrigger.io.star (module) outrigger.psi (module) outrigger.psi.compute (module) outrigger.region (module) outrigger.tests (module) outrigger.tests.conftest (module)

outrigger.tests.index (module) outrigger.tests.index.test_adjacencies (module) outrigger.tests.index.test_events (module) outrigger.tests.index.test_region (module) outrigger.tests.io (module) outrigger.tests.io.test_bam (module) outrigger.tests.io.test_gtf (module) outrigger.tests.io.test_star (module) outrigger.tests.psi (module) outrigger.tests.psi.test_compute (module) outrigger.tests.test_commandline (module) outrigger.tests.validate (module) outrigger.tests.validate.test_check_splice_sites (module) outrigger.util (module) outrigger.validate (module) outrigger.validate.check_splice_sites (module) outrigger_folder() (in module outrigger.tests.conftest) overlaps() (outrigger.region.Region method)

P

progress() (in module outrigger.util) Psi (class in outrigger.commandline) psi() (outrigger.commandline.CommandLine method)

psi_csv() (in module outrigger.tests.psi.test_compute) psi_df() (in module outrigger.tests.psi.test_compute) psi_folder (outrigger.commandline.Psi attribute)

R

read_intermediate_junctions() (in module outrigger.tests.io.test_bam) read_multiple_bams() (in module outrigger.io.bam) read_multiple_sj_out_tab() (in module outrigger.io.star) read_sj_out_tab() (in module outrigger.io.star) read_splice_sites() (in module outrigger.validate.check_splice_sites) reads2d() (in module outrigger.tests.psi.test_compute)

reads_col (outrigger.commandline.Psi attribute) (outrigger.commandline.Subcommand attribute) Region (class in outrigger.region) region (outrigger.region.Region attribute) region() (in module outrigger.tests.index.test_events) required_cols (outrigger.commandline.Psi attribute) resume (outrigger.commandline.Subcommand attribute)

S

sample_id_col (outrigger.commandline.Psi attribute) simulated() (in module outrigger.tests.conftest) simulated_chromsizes() (in module outrigger.tests.validate.test_check_splice_sites) simulated_fasta() (in module outrigger.tests.validate.test_check_splice_sites) simulated_outrigger_index() (in module outrigger.tests.conftest) simulated_outrigger_mxe() (in module outrigger.tests.conftest) simulated_outrigger_output() (in module outrigger.tests.conftest) simulated_outrigger_psi() (in module outrigger.tests.conftest) simulated_outrigger_se() (in module outrigger.tests.conftest) simulated_unprocessed() (in module outrigger.tests.conftest) single_bam_combined_uniquely_multi_csv() (in module outrigger.tests.io.test_bam) single_bam_final_junction_reads_table_csv() (in module outrigger.tests.io.test_bam) single_event_summary_csv() (in module outrigger.tests.psi.test_compute) single_exon_alternative_events() (outrigger.index.events.SpliceGraph method) sj_filenames() (in module outrigger.tests.conftest) sj_out_tab (outrigger.commandline.Subcommand attribute) sj_out_tab() (in module outrigger.tests.io.test_star) skipped_exon_events() (outrigger.tests.index.test_events.TestSpliceGraph method) skipped_exon_junction_reads_for_rejecting() (in module outrigger.tests.psi.test_compute) skipped_exon_junction_reads_for_rejecting_csv() (in module outrigger.tests.psi.test_compute) snap25_exon() (outrigger.tests.index.test_adjacencies.TestExonJunctionAdjacencies method)

snap25_exon_id() (in module outrigger.tests.conftest) splice_abbrevs (outrigger.commandline.Index attribute) splice_graph() (outrigger.tests.index.test_events.TestSpliceGraph method) splice_junction_csv() (in module outrigger.tests.io.test_star) splice_junction_reads() (in module outrigger.tests.psi.test_compute) splice_junction_reads_csv() (in module outrigger.tests.psi.test_compute) splice_site_str_to_tuple() (in module outrigger.validate.check_splice_sites) splice_type() (in module outrigger.tests.conftest) splice_type_folders (outrigger.commandline.Psi attribute) SpliceGraph (class in outrigger.index.events) SplicingAnnotator (class in outrigger.io.gtf) start (outrigger.region.Region attribute) stop (outrigger.region.Region attribute) strand (outrigger.region.Region attribute) strand() (in module outrigger.tests.conftest) strand_name() (outrigger.tests.index.test_events.TestEventMaker method) stringify_location() (in module outrigger.index.events) Subcommand (class in outrigger.commandline) SubcommandAfterIndex (class in outrigger.commandline) suffix_template() (in module outrigger.tests.io.test_bam) summary_csv() (in module outrigger.tests.psi.test_compute) summary_df() (in module outrigger.tests.psi.test_compute)

T

tasic2016() (in module outrigger.tests.conftest) tasic2016_bam() (in module outrigger.tests.conftest) tasic2016_gtf() (in module outrigger.tests.conftest) tasic2016_intermediate() (in module outrigger.tests.conftest) tasic2016_intermediate_bam() (in module outrigger.tests.conftest) tasic2016_intermediate_psi() (in module outrigger.tests.conftest) tasic2016_outrigger_junctions() (in module outrigger.tests.conftest) tasic2016_outrigger_output() (in module outrigger.tests.conftest) tasic2016_outrigger_output_bam() (in module outrigger.tests.conftest) tasic2016_outrigger_output_index() (in module outrigger.tests.conftest) tasic2016_outrigger_output_psi() (in module outrigger.tests.conftest) tasic2016_sj_out_tab() (in module outrigger.tests.conftest) tasic2016_unprocessed() (in module outrigger.tests.conftest) test___eq() (outrigger.tests.index.test_region.TestRegion method) test___eq_not_region() (outrigger.tests.index.test_region.TestRegion method) test___init() (outrigger.tests.index.test_adjacencies.TestExonJunctionAdjacencies method) (outrigger.tests.index.test_region.TestRegion method) test___init__() (outrigger.tests.index.test_events.TestSpliceGraph method) (outrigger.tests.test_commandline.TestSubcommand method) test___init_missing_required_column() (outrigger.tests.index.test_adjacencies.TestExonJunctionAdjacencies method) test___init_region_name() (outrigger.tests.index.test_region.TestRegion method) test___init_start_larger_than_stop() (outrigger.tests.index.test_region.TestRegion method) test___len() (outrigger.tests.index.test_region.TestRegion method) test___neq() (outrigger.tests.index.test_region.TestRegion method) test___str() (outrigger.tests.index.test_region.TestRegion method) test___str_with_region_name() (outrigger.tests.index.test_region.TestRegion method) test__adjacent_junctions_single_exon() (outrigger.tests.index.test_adjacencies.TestExonJunctionAdjacencies method) test__check_unequal_read_coverage() (in module outrigger.tests.psi.test_compute) test__choose_strand_and_sum() (in module outrigger.tests.io.test_bam) test__combine_uniquely_multi() (in module outrigger.tests.io.test_bam) test__get_junction_reads() (in module outrigger.tests.io.test_bam) test__junctions_genome_adjacent_to_exon() (outrigger.tests.index.test_adjacencies.TestExonJunctionAdjacencies method) test__maybe_parallelize_psi() (in module outrigger.tests.psi.test_compute) test__mutually_exclusive_exon() (outrigger.tests.index.test_events.TestSpliceGraph method) test__report_read_positions() (in module outrigger.tests.io.test_bam) test__single_event_psi() (in module outrigger.tests.psi.test_compute) test__single_isoform_maybe_reject() (in module outrigger.tests.psi.test_compute) test__single_junction_exon_triple() (outrigger.tests.index.test_adjacencies.TestExonJunctionAdjacencies method) test__skipped_exon() (outrigger.tests.index.test_events.TestSpliceGraph method) test__start() (outrigger.tests.index.test_region.TestRegion method) test__stop() (outrigger.tests.index.test_region.TestRegion method) test__to_stranded_transcript_adjacency() (outrigger.tests.index.test_adjacencies.TestExonJunctionAdjacencies method) test_a3ss() (outrigger.tests.index.test_events.TestEventMaker method) test_a5ss() (outrigger.tests.index.test_events.TestEventMaker method) test_afe() (outrigger.tests.index.test_events.TestEventMaker method)

test_ale() (outrigger.tests.index.test_events.TestEventMaker method) test_bam_to_junction_reads_table() (in module outrigger.tests.io.test_bam) test_calculate_psi() (in module outrigger.tests.psi.test_compute) test_create_db() (in module outrigger.tests.io.test_gtf) test_exons_one_junction_upstream() (outrigger.tests.index.test_events.TestSpliceGraph method) test_exons_two_junctions_downstream() (outrigger.tests.index.test_events.TestSpliceGraph method) test_finding_events() (outrigger.tests.index.test_events.TestEventMaker method) test_help() (outrigger.tests.test_commandline.TestCommandLine method) test_init() (outrigger.tests.index.test_events.TestEventMaker method) test_int_to_intron_motif() (in module outrigger.tests.io.test_star) test_junctions_between_exons() (outrigger.tests.index.test_events.TestSpliceGraph method) test_main_index() (outrigger.tests.test_commandline.TestCommandLine method) test_main_index_bam() (outrigger.tests.test_commandline.TestCommandLine method) test_main_index_parallelized() (outrigger.tests.test_commandline.TestCommandLine method) test_main_index_reads_csv() (outrigger.tests.test_commandline.TestCommandLine method) test_main_psi() (outrigger.tests.test_commandline.TestCommandLine method) test_main_psi_bam() (outrigger.tests.test_commandline.TestCommandLine method) test_main_psi_parallelized() (outrigger.tests.test_commandline.TestCommandLine method) test_main_validate() (outrigger.tests.test_commandline.TestCommandLine method) test_main_version() (outrigger.tests.test_commandline.TestCommandLine method) test_make_metadata() (in module outrigger.tests.io.test_star) test_maybe_read_chromsizes() (in module outrigger.tests.validate.test_check_splice_sites) test_neighboring_exons() (outrigger.tests.index.test_adjacencies.TestExonJunctionAdjacencies method) test_no_arguments() (outrigger.tests.test_commandline.TestCommandLine method) test_overlaps_false_different_chrom() (outrigger.tests.index.test_region.TestRegion method) test_overlaps_false_same_chrom() (outrigger.tests.index.test_region.TestRegion method) test_overlaps_true() (outrigger.tests.index.test_region.TestRegion method) test_read_multiple_bams() (in module outrigger.tests.io.test_bam) test_read_multiple_sj_out_tab() (in module outrigger.tests.io.test_star) test_read_sj_out_tab() (in module outrigger.tests.io.test_star) test_read_splice_sites() (in module outrigger.tests.validate.test_check_splice_sites) test_single_exon_alternative_events() (outrigger.tests.index.test_events.TestSpliceGraph method) test_splice_site_str_to_tuple() (in module outrigger.tests.validate.test_check_splice_sites) test_stringify_location() (in module outrigger.tests.index.test_events) TestCommandLine (class in outrigger.tests.test_commandline) TestEventMaker (class in outrigger.tests.index.test_events) TestExonJunctionAdjacencies (class in outrigger.tests.index.test_adjacencies) TestRegion (class in outrigger.tests.index.test_region) TestSpliceGraph (class in outrigger.tests.index.test_events) TestSubcommand (class in outrigger.tests.test_commandline) timestamp() (in module outrigger.util) to_bed_format() (outrigger.region.Region method) to_zero_based() (outrigger.region.Region method) transcripts() (in module outrigger.tests.index.test_events) transform() (in module outrigger.io.gtf)

U

uniquely() (in module outrigger.tests.io.test_bam) uniquely_csv() (in module outrigger.tests.io.test_bam)

uniquely_summed_csv() (in module outrigger.tests.io.test_bam) upstream_downstream_exons() (outrigger.index.adjacencies.ExonJunctionAdjacencies method) Usage

V

Validate (class in outrigger.commandline)

validate() (outrigger.commandline.CommandLine method) validate_junction_reads_data() (outrigger.commandline.Psi method)

W

write_de_novo_exons() (outrigger.index.adjacencies.ExonJunctionAdjacencies method)

write_new_gtf() (outrigger.commandline.Index method)