ontmont

• ontmont package
  • Submodules
  • ontmont.bundle module
    • make_brk_supports()
    • make_brk_table()
    • make_brks_bundle()
    • make_seg_table()
    • make_tra_table()
  • ontmont.cli module
  • ontmont.collect module
    • extract_split_alignments()
    • find_presence_of_matching_sv()
    • fix_lower_support_coordinates()
    • get_breakpoint_support_from_bundle()
    • get_normalized_sv()
    • get_svtype()
    • make_brks_bundle()
    • make_tumor_sv_table()
    • map_similar_coordinate_to_higher_rank()
    • normalize_sv_table()
    • pull_breakpoints_from_bam_files()
    • pull_breakpoints_from_reads_in_sv_regions()
    • pull_sv_supporting_reads_from_bundle()
  • ontmont.datatypes module
    • Breakpoint
      • Breakpoint.chroms
      • Breakpoint.get_breakpoint_seqs()
    • BreakpointChain
      • BreakpointChain.get_segments()
      • BreakpointChain.get_transitions()
    • BreakpointPair
    • Sample
      • Sample.long_samples
      • Sample.sample2group
      • Sample.sample2short
    • Segments
      • Segments.get_list()
    • SplitAlignment
      • SplitAlignment.extract_cigar_field()
      • SplitAlignment.get_cigar_tuples()
    • Transitions
      • Transitions.get_list()
    • get_breakpoint_seqs()
  • ontmont.irs module
    • align_two_sequences()
    • calc_distance_score()
    • calc_pval_bilateral_ir()
    • calc_pval_holliday()
    • calc_pval_onesided_ir()
    • calc_pval_segmental_ir()
    • get_best_holliday_junctions()
    • get_best_ir_within_breakpoints()
    • get_best_ir_within_segment()
    • get_best_onesided_ir()
    • get_breakpoint_pair_seq_data()
    • get_onesided_ir()
    • is_holliday_junction()
    • overlaps()
  • ontmont.plot module
    • add_gene_annotations()
    • add_sv_legend_to_axes()
    • convert_tupleproxy_to_pyranges()
    • extract_vaf_from_annotated_sv_table()
    • fix_coordinate_xticklabels()
    • fix_yticks_with_integers()
    • get_chrom_xlims()
    • get_chromosomes_from_bundle()
    • get_cn_blocks_for_read_xlim()
    • get_edgecolor()
    • get_gene_repr_exons()
    • get_repr_transcript_id()
    • get_sv_table_chroms()
    • get_transcript_exons()
    • get_unique_sv_with_support()
    • is_overlap()
    • make_axes_for_breakpoints()
    • make_spline_coordinates()
    • parse_gtf_region()
    • plot_cn_on_axes()
    • plot_gene_annotations()
    • plot_jabba_cn()
    • plot_quasijabba()
    • plot_segments_on_axes()
    • plot_sv_lines_on_cn()
    • plot_svs_to_cn_segments()
    • plot_transition_on_axes()
    • plot_vaf_cn_sv_for_reads()
    • plot_vaf_on_axes()
  • ontmont.process module
    • filter_sv_by_clone()
    • merge_cn_segments()
    • update_blocks_and_reset_prev()
  • ontmont.utils module
    • enumerate_breakpoints()
    • extract_split_alignments()
    • filter_breakpoints_at_contig_ends()
    • filter_sv_with_breakpoint_at_contig_ends()
    • get_chromosomes_to_process()
    • get_secondaries()
    • is_breakpoints_not_sorted()
    • make_split_read_table()
    • remove_duplicates_from_tra_table()
    • reverse_complement()
    • shuffle_seq()
  • Module contents