Index

A

add_exon_sequences() (in module thoraxe.transcript_info.transcript_info) add_protein_seq() (in module thoraxe.transcript_info.transcript_info) add_s_exon_phases_and_coordinates() (in module thoraxe.thoraxe)

add_sequences() (in module thoraxe.add_transcripts.add_transcripts) add_to_exontable() (in module thoraxe.add_transcripts.add_transcripts) add_to_tsl() (in module thoraxe.add_transcripts.add_transcripts) align() (in module thoraxe.transcript_info.exon_clustering)

B

bases_to_complete_next_codon() (in module thoraxe.transcript_info.phases)

bases_to_complete_previous_codon() (in module thoraxe.transcript_info.phases) block_type (thoraxe.subexons.alignment.ProblematicSubexonBlock property)

C

calculate_phase() (in module thoraxe.transcript_info.phases) check_input() (in module thoraxe.add_transcripts.add_transcripts) check_order_and_phases() (in module thoraxe.transcript_info.phases) check_species_name() (in module thoraxe.utils.species) cluster2str() (in module thoraxe.transcript_info.clusters) cluster_subexon_blocks() (in module thoraxe.subexons.alignment) ColCluster (class in thoraxe.subexons.alignment) ColPattern (class in thoraxe.subexons.alignment) column_clusters() (in module thoraxe.subexons.alignment) column_patterns() (in module thoraxe.subexons.alignment) components (thoraxe.subexons.subexons.Interval property)

conserved_ases() (in module thoraxe.subexons.ases) coverage() (in module thoraxe.transcript_info.exon_clustering) coverage_shortest() (in module thoraxe.transcript_info.exon_clustering) create_ases_table() (in module thoraxe.subexons.ases) create_chimeric_msa() (in module thoraxe.thoraxe) create_chimeric_sequences() (in module thoraxe.subexons.alignment) create_msa_matrix() (in module thoraxe.subexons.alignment) create_python_structure() (in module thoraxe.subexons.plot) create_subexon_matrix() (in module thoraxe.subexons.alignment) create_subexon_table() (in module thoraxe.subexons.subexons) create_subfolder() (in module thoraxe.utils.folders)

D

delete_badquality_sequences() (in module thoraxe.transcript_info.transcript_info) delete_identical_sequences() (in module thoraxe.transcript_info.transcript_info) delete_incomplete_sequences() (in module thoraxe.transcript_info.transcript_info) delete_padding() (in module thoraxe.subexons.alignment)

delete_subexons() (in module thoraxe.subexons.alignment) detect_ases() (in module thoraxe.subexons.ases) dictseq2fasta() (in module thoraxe.transcript_query.transcript_query) disintegration() (in module thoraxe.subexons.alignment) disjoint_intervals() (in module thoraxe.subexons.subexons)

E

end (thoraxe.subexons.alignment.ColPattern property) (thoraxe.subexons.subexons.Interval property)

end_phase_previous_exon() (in module thoraxe.transcript_info.phases) exon_clustering() (in module thoraxe.transcript_info.exon_clustering) exontable (thoraxe.add_transcripts.add_transcripts.Paths property)

F

fill_clusters() (in module thoraxe.transcript_info.clusters) filter_ortho() (in module thoraxe.transcript_query.transcript_query)

find_identical_exons() (in module thoraxe.transcript_info.transcript_info) find_identical_sequences() (in module thoraxe.transcript_info.transcript_info)

G

gap_block_end (thoraxe.subexons.alignment.ProblematicSubexonBlock property) gap_block_start (thoraxe.subexons.alignment.ProblematicSubexonBlock property) gene2species() (in module thoraxe.subexons.alignment) generic_ensembl_rest_request() (in module thoraxe.transcript_query.transcript_query) Genes (thoraxe.subexons.ases.PathData property) get_biomart_exons_annot() (in module thoraxe.transcript_query.transcript_query) get_consensus() (in module thoraxe.subexons.alignment) get_exons_sequences() (in module thoraxe.transcript_query.transcript_query) get_gene_ids() (in module thoraxe.subexons.alignment) get_geneids_from_symbol() (in module thoraxe.transcript_query.transcript_query) get_genetree() (in module thoraxe.transcript_query.transcript_query) get_listofexons() (in module thoraxe.transcript_query.transcript_query) get_listoftranscripts() (in module thoraxe.transcript_query.transcript_query) get_orthologs() (in module thoraxe.transcript_query.transcript_query)

get_output_paths() (in module thoraxe.add_transcripts.add_transcripts) get_s_exon2char() (in module thoraxe.subexons.phylosofs) get_s_exon_msas() (in module thoraxe.thoraxe) get_s_exons() (in module thoraxe.thoraxe) get_species_list() (in module thoraxe.utils.species) get_subexon_boundaries() (in module thoraxe.subexons.alignment) get_subexons() (in module thoraxe.thoraxe) get_submsa() (in module thoraxe.subexons.alignment) get_tidy_table() (in module thoraxe.subexons.tidy) get_transcript2phylosofs() (in module thoraxe.subexons.phylosofs) get_transcript_scores() (in module thoraxe.subexons.ases) get_transcripts() (in module thoraxe.thoraxe) get_transcripts_orthologs() (in module thoraxe.transcript_query.transcript_query) get_unaligned_regions() (in module thoraxe.subexons.rescue)

I

impute_missing_s_exon() (in module thoraxe.subexons.alignment) inform_about_deletions() (in module thoraxe.transcript_info.clusters) input (thoraxe.add_transcripts.add_transcripts.Paths property)

Interval (class in thoraxe.subexons.subexons) is_esemble_id() (in module thoraxe.transcript_query.transcript_query) is_windows() (in module thoraxe.utils.windows)

L

lodict2csv() (in module thoraxe.transcript_query.transcript_query)

M

main() (in module thoraxe.add_transcripts.add_transcripts) (in module thoraxe.thoraxe) (in module thoraxe.transcript_query.transcript_query) merge_clusters() (in module thoraxe.thoraxe) merge_identical_exons() (in module thoraxe.transcript_info.transcript_info) modify_subexon_cluster() (in module thoraxe.subexons.rescue) module thoraxe thoraxe.add_transcripts thoraxe.add_transcripts.add_transcripts thoraxe.subexons thoraxe.subexons.alignment thoraxe.subexons.ases thoraxe.subexons.graph thoraxe.subexons.phylosofs thoraxe.subexons.plot thoraxe.subexons.rescue thoraxe.subexons.subexons thoraxe.subexons.tidy thoraxe.thoraxe thoraxe.transcript_info thoraxe.transcript_info.clusters thoraxe.transcript_info.exon_clustering thoraxe.transcript_info.phases thoraxe.transcript_info.transcript_info thoraxe.transcript_query thoraxe.transcript_query.transcript_query thoraxe.utils thoraxe.utils.folders thoraxe.utils.species thoraxe.utils.split thoraxe.utils.windows thoraxe.version

move_block() (in module thoraxe.subexons.alignment) move_problematic_block_clusters() (in module thoraxe.subexons.alignment) move_subexon_block() (in module thoraxe.subexons.alignment) msa2sequences() (in module thoraxe.subexons.alignment) msa_matrices() (in module thoraxe.subexons.alignment)

N

nodes_and_edges2genes_and_transcripts() (in module thoraxe.subexons.graph)

P

parse_command_line() (in module thoraxe.add_transcripts.add_transcripts) (in module thoraxe.thoraxe) (in module thoraxe.transcript_query.transcript_query) PathData (class in thoraxe.subexons.ases) Paths (class in thoraxe.add_transcripts.add_transcripts) pattern (thoraxe.subexons.alignment.ColPattern property)

percent_identity() (in module thoraxe.transcript_info.exon_clustering) phylosofs_inputs() (in module thoraxe.subexons.phylosofs) plot_msa_subexons() (in module thoraxe.subexons.plot) problematic_block_clusters() (in module thoraxe.subexons.alignment) problematic_subexon_blocks() (in module thoraxe.subexons.alignment) ProblematicSubexonBlock (class in thoraxe.subexons.alignment) prune_tree() (in module thoraxe.subexons.phylosofs)

R

read_exon_file() (in module thoraxe.transcript_info.transcript_info) read_fasta() (in module thoraxe.add_transcripts.add_transcripts) read_msa_fasta() (in module thoraxe.subexons.alignment) read_splice_graph() (in module thoraxe.subexons.ases)

read_transcript_info() (in module thoraxe.transcript_info.transcript_info) read_tsl_file() (in module thoraxe.transcript_info.transcript_info) resume_seq() (in module thoraxe.subexons.alignment) run_aligner() (in module thoraxe.subexons.alignment)

S

save_ensembl_version() (in module thoraxe.transcript_query.transcript_query) save_s_exons() (in module thoraxe.subexons.alignment) score_solution() (in module thoraxe.subexons.alignment) sequence_index (thoraxe.subexons.alignment.ProblematicSubexonBlock property) sequences (thoraxe.add_transcripts.add_transcripts.Paths property) set_to_delete() (in module thoraxe.transcript_info.clusters) sort_species() (in module thoraxe.subexons.alignment) splice_graph_gml() (in module thoraxe.subexons.graph) split_exons() (in module thoraxe.utils.split) split_lengths() (in module thoraxe.utils.split)

split_seqs() (in module thoraxe.utils.split) start (thoraxe.subexons.alignment.ColPattern property) (thoraxe.subexons.subexons.Interval property) store_cluster() (in module thoraxe.transcript_info.transcript_info) subexon (thoraxe.subexons.alignment.ProblematicSubexonBlock property) subexon_block_end (thoraxe.subexons.alignment.ProblematicSubexonBlock property) subexon_block_start (thoraxe.subexons.alignment.ProblematicSubexonBlock property) subexon_blocks (thoraxe.subexons.alignment.ProblematicSubexonBlock property) subexon_connectivity() (in module thoraxe.subexons.alignment) subexon_rescue_phase() (in module thoraxe.subexons.rescue)

T

thoraxe module thoraxe.add_transcripts module thoraxe.add_transcripts.add_transcripts module thoraxe.subexons module thoraxe.subexons.alignment module thoraxe.subexons.ases module thoraxe.subexons.graph module thoraxe.subexons.phylosofs module thoraxe.subexons.plot module thoraxe.subexons.rescue module thoraxe.subexons.subexons module thoraxe.subexons.tidy module thoraxe.thoraxe module thoraxe.transcript_info module

thoraxe.transcript_info.clusters module thoraxe.transcript_info.exon_clustering module thoraxe.transcript_info.phases module thoraxe.transcript_info.transcript_info module thoraxe.transcript_query module thoraxe.transcript_query.transcript_query module thoraxe.utils module thoraxe.utils.folders module thoraxe.utils.species module thoraxe.utils.split module thoraxe.utils.windows module thoraxe.version module Transcripts (thoraxe.subexons.ases.PathData property) tsl (thoraxe.add_transcripts.add_transcripts.Paths property)

U

update_subexon_table() (in module thoraxe.thoraxe)

update_to_merge_list() (in module thoraxe.subexons.subexons)

W

write_tsl_file() (in module thoraxe.transcript_query.transcript_query)