Index

A

ABOUT (in module coalispr.tk_gui.gui_constants) ACOL (in module coalispr.resources.constant) add_sample_controller() (coalispr.bedgraph_analyze.bam_keys_collators.Bam_samples_collator class method) add_widget() (coalispr.tk_gui.gui_widgets.opt.Options_frame method) (coalispr.tk_gui.gui_widgets.opt2.Subcommand_frame method) AEC (in module coalispr.resources.constant) Ago ALC (in module coalispr.resources.constant) ALL (in module coalispr.resources.constant) all_exps() (in module coalispr.bedgraph_analyze.experiment) ALPH (in module coalispr.resources.constant) anchored_text() (in module coalispr.resources.plot_utilities) ANNOTALPH (in module coalispr.resources.constant)

annotate() (in module coalispr.coalispr) annotate_clust_file() (in module coalispr.count_analyze.annot) annotate_count_frame() (in module coalispr.count_analyze.annot) annotate_libtotals() (in module coalispr.count_analyze.annot) arg (coalispr.tk_gui.gui_widgets.opt2.Option_widget attribute), [1] args (coalispr.tk_gui.gui_widgets.opt2.Option_widget attribute), [1] args_dict (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1] argvar (coalispr.tk_gui.gui_widgets.opt2.Option_widget attribute), [1] argvars (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1] assemble_groupsamples() (in module coalispr.resources.dialog) AXCOL (in module coalispr.resources.constant) AXCOL2 (in module coalispr.resources.constant) AXLIMS (in module coalispr.resources.constant)

B

BACKEND (in module coalispr.resources.constant) background backup_pickle_to_tsv() (in module coalispr.bedgraph_analyze.store) BAK (in module coalispr.resources.constant) bam BAM (in module coalispr.resources.constant) BAM2BG (in module coalispr.resources.constant) BAM2BGNAM (in module coalispr.resources.constant) Bam_collector (class in coalispr.bedgraph_analyze.process_bamdata) Bam_countprocessor (class in coalispr.bedgraph_analyze.process_bamdata) Bam_sample_base_controller (class in coalispr.bedgraph_analyze.bam_sample_counters) Bam_sample_counter_controller (class in coalispr.bedgraph_analyze.bam_sample_counters) Bam_sample_region_counter_controller (class in coalispr.bedgraph_analyze.bam_sample_counters) Bam_samples_collator (class in coalispr.bedgraph_analyze.bam_keys_collators) bamfiles (coalispr.bedgraph_analyze.process_bamdata.Bam_collector attribute), [1] BAMHIGH (in module coalispr.resources.constant) bamkeys (coalispr.bedgraph_analyze.process_bamdata.Bam_collector attribute), [1] BAMLOW (in module coalispr.resources.constant) bampath (coalispr.bedgraph_analyze.process_bamdata.Bam_countprocessor attribute) bampeak (coalispr.bedgraph_analyze.process_bamdata.Bam_countprocessor attribute) BAMPEAK (in module coalispr.resources.constant) bams (coalispr.bedgraph_analyze.process_bamdata.Bam_countprocessor attribute) bamstart (coalispr.bedgraph_analyze.process_bamdata.Bam_countprocessor attribute) BAMSTART (in module coalispr.resources.constant) barcode barlinewidth (coalispr.count_analyze.panel_plotters.BrokenLengthPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.PanelPlotter attribute) barwidth (coalispr.count_analyze.panel_plotters.CountPanelPlotter attribute)

BASEDIR (in module coalispr.resources.constant) bash BCKGRCOL (in module coalispr.resources.constant) BCO (in module coalispr.resources.constant) beancollector (coalispr.bedgraph_analyze.process_bamdata.Bam_countprocessor attribute) bedgraph BEDGRAPH (in module coalispr.resources.constant) bedgraphs_from_xtra_bamdata() (in module coalispr.bedgraph_analyze.process_bamdata) bgconvert_file() (in module coalispr.resources.share.convert_plusmin_bedgraph_to_plusplus) bin bin_bedgraphs() (in module coalispr.bedgraph_analyze.process_bedgraphs) binary numbers BINN (in module coalispr.resources.constant) binner_dict (coalispr.bedgraph_analyze.bam_keys_collators.Bam_samples_collator attribute) binners (coalispr.bedgraph_analyze.bam_sample_counters.Bam_sample_base_controller attribute), [1] (coalispr.bedgraph_analyze.bam_sample_counters.Bam_sample_counter_controller attribute), [1] (coalispr.bedgraph_analyze.bam_sample_counters.Bam_sample_region_counter_controller attribute), [1] BINNERS (in module coalispr.bedgraph_analyze.bam_keys_collators) BinPanelPlotter (class in coalispr.count_analyze.panel_plotters) bins (coalispr.bedgraph_analyze.process_bamdata.Bam_countprocessor attribute) BINS (in module coalispr.resources.constant) bins_sum() (in module coalispr.resources.utilities) BINSTEP (in module coalispr.resources.constant) biological experiment biological replicate BIOR (in module coalispr.tk_gui.gui_constants) break_xaxis() (in module coalispr.resources.plot_utilities) BREG (in module coalispr.resources.constant) BrokenLengthPanelPlotter (class in coalispr.count_analyze.panel_plotters)

C

canvas_scroll_command() (coalispr.tk_gui.gui_widgets.opt.Options_frame method) canvas_scrollbar (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1] capit_label() (in module coalispr.resources.plot_utilities) CAT_D (in module coalispr.resources.constant) CAT_M (in module coalispr.resources.constant) CAT_R (in module coalispr.resources.constant) CAT_S (in module coalispr.resources.constant) CAT_U (in module coalispr.resources.constant) CATEGORY (in module coalispr.resources.constant) cDNA change_subcommand() (coalispr.tk_gui.gui_widgets.opt2.Subcommand_frame method) chdir_current_exp() (in module coalispr.tk_gui.gui_utilities) check_bam_file() (coalispr.bedgraph_analyze.process_bamdata.Bam_countprocessor class method) check_newpath() (in module coalispr.resources.utilities) checkset() (in module coalispr.bedgraph_analyze.collect_bedgraphs) checkSRCDIR() (in module coalispr.bedgraph_analyze.collect_bedgraphs) choice (coalispr.tk_gui.gui_widgets.opt2.Option_widget attribute), [1] choices (coalispr.tk_gui.gui_widgets.opt2.Subcommand_frame attribute), [1] choose_frame (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1] chr_test() (in module coalispr.bedgraph_analyze.genom) chrnam (coalispr.bedgraph_analyze.genom.SegmentTrack attribute) (coalispr.bedgraph_analyze.genom.Track attribute), [1] chrno (coalispr.resources.share.ncfasta2gtf.Gtfline attribute), [1] chrom_region() (in module coalispr.resources.utilities) CHROMFIG (in module coalispr.resources.constant) CHROMLBL (in module coalispr.resources.constant) chroms() (in module coalispr.bedgraph_analyze.genom) CHRXTRA (in module coalispr.resources.constant) chrxtra() (in module coalispr.resources.utilities) cigar CIGARCHK (in module coalispr.resources.constant) cigchk (coalispr.bedgraph_analyze.process_bamdata.Bam_countprocessor attribute) CIGFM (in module coalispr.resources.constant) CIGPD (in module coalispr.resources.constant) CKEY1 (in module coalispr.resources.constant) CKEY2 (in module coalispr.resources.constant) CKEY3 (in module coalispr.resources.constant) CKEY4 (in module coalispr.resources.constant) clean_dict() (in module coalispr.resources.utilities) clean_fasta() (in module coalispr.resources.share.clean_fasta) clean_file() (in module coalispr.resources.share.no_empty_fa) clean_igb() (in module coalispr.resources.share.gtf_frm_tsv) CLI Cli_menu (class in coalispr.tk_gui.gui_widgets.menu_main) CLUSTGR (in module coalispr.resources.constant) CLUSTVIS (in module coalispr.resources.constant) CNTCDNA (in module coalispr.resources.constant) CNTGAP (in module coalispr.resources.constant) CNTLABELS (in module coalispr.resources.constant) cntlabl (coalispr.bedgraph_analyze.bam_sample_counters.Sample_length_counter attribute) (coalispr.bedgraph_analyze.bam_sample_counters.Sample_multimap_counter attribute) CNTREAD (in module coalispr.resources.constant) CNTRS (in module coalispr.resources.constant) CNTSKIP (in module coalispr.resources.constant) coalispr module coalispr() (in module coalispr.coalispr) coalispr.bedgraph_analyze module coalispr.bedgraph_analyze.bam_keys_collators module coalispr.bedgraph_analyze.bam_sample_counters module coalispr.bedgraph_analyze.bedgraph_plots module coalispr.bedgraph_analyze.collect_bedgraphs module coalispr.bedgraph_analyze.compare module coalispr.bedgraph_analyze.experiment module coalispr.bedgraph_analyze.genom module coalispr.bedgraph_analyze.info_plots module coalispr.bedgraph_analyze.process_bamdata module coalispr.bedgraph_analyze.process_bedgraphs module coalispr.bedgraph_analyze.references module coalispr.bedgraph_analyze.store module coalispr.bedgraph_analyze.unselected module coalispr.coalispr module coalispr.count_analyze module coalispr.count_analyze.annot module coalispr.count_analyze.countfile_plots module coalispr.count_analyze.filter_data module coalispr.count_analyze.groupcompare_plots module coalispr.count_analyze.load_countfile module coalispr.count_analyze.panel_plotters module coalispr.count_analyze.regioncount_plots module coalispr.resources module coalispr.resources.cmd_parser module coalispr.resources.constant module coalispr.resources.constant_in module coalispr.resources.constant_in.make_constant module coalispr.resources.dialog module coalispr.resources.numeric module coalispr.resources.plot_utilities module coalispr.resources.profilehooks module coalispr.resources.profilehooks.profilehooks module coalispr.resources.profilehooks.profilehooks_enable module coalispr.resources.share module coalispr.resources.share.clean_fasta module

coalispr.resources.share.cols_from_csv_to_tab module coalispr.resources.share.convert_gff3 module coalispr.resources.share.convert_plusmin_bedgraph_to_plusplus module coalispr.resources.share.genbank2gtf module coalispr.resources.share.get_smallRNAs_and_targets module coalispr.resources.share.gtf_frm_tsv module coalispr.resources.share.ncfasta2gtf module coalispr.resources.share.no_empty_fa module coalispr.resources.share.reduce_gtf module coalispr.resources.share.revseq module coalispr.resources.share.sub_gtf module coalispr.resources.utilities module coalispr.tk_gui module coalispr.tk_gui.customtkinter module coalispr.tk_gui.customtkinter.font_manager module coalispr.tk_gui.gui_constants module coalispr.tk_gui.gui_utilities module coalispr.tk_gui.gui_widgets module coalispr.tk_gui.gui_widgets.menu_main module coalispr.tk_gui.gui_widgets.opt module coalispr.tk_gui.gui_widgets.opt2 module coalispr.tk_gui.tk_coalispr module Coalispr_app (class in coalispr.tk_gui.tk_coalispr) collapsed COLLAPSED (in module coalispr.resources.constant) collect_bamfiles() (coalispr.bedgraph_analyze.process_bamdata.Bam_collector class method) collect_bedgraphs() (in module coalispr.bedgraph_analyze.collect_bedgraphs) collect_coseqframes() (in module coalispr.count_analyze.filter_data) collect_limits() (in module coalispr.resources.dialog) collect_references() (in module coalispr.bedgraph_analyze.collect_bedgraphs) collected_counters (coalispr.bedgraph_analyze.process_bamdata.Bam_countprocessor attribute) COLLR (in module coalispr.resources.constant) colr (coalispr.tk_gui.gui_widgets.opt2.Option_widget attribute), [1] cols (coalispr.bedgraph_analyze.process_bamdata.Bam_countprocessor attribute) COMBI (in module coalispr.resources.constant) combine_counters() (coalispr.bedgraph_analyze.bam_keys_collators.Bam_samples_collator class method) comm_description (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1] command (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1] COMMAND_DESCRIPTIONS (in module coalispr.tk_gui.gui_constants) command_field (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1] command_frame (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1] Command_frames (class in coalispr.tk_gui.gui_widgets.menu_main) command_frames (coalispr.tk_gui.gui_widgets.menu_main.Command_frames attribute) command_submit (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1] command_var (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1] COMMANDS (in module coalispr.tk_gui.gui_constants) compare_5nt_lengths() (in module coalispr.count_analyze.groupcompare_plots) compare_exp_bins() (in module coalispr.count_analyze.countfile_plots) compare_exp_lengths() (in module coalispr.count_analyze.countfile_plots) compare_exp_mulmaps() (in module coalispr.count_analyze.countfile_plots) compare_libtotals() (in module coalispr.count_analyze.countfile_plots) compare_un_spec_lengths() (in module coalispr.count_analyze.countfile_plots) compare_un_spec_mulmaps() (in module coalispr.count_analyze.countfile_plots) comparereads (coalispr.bedgraph_analyze.bam_sample_counters.Bam_sample_region_counter_controller attribute), [1] (coalispr.bedgraph_analyze.process_bamdata.Bam_countprocessor attribute) CONDITION (in module coalispr.resources.constant) CONDITIONS (in module coalispr.resources.constant) CONFBASE (in module coalispr.resources.constant) CONFFILE (in module coalispr.resources.constant) CONFFOLDER (in module coalispr.resources.constant) CONFIG (in module coalispr.resources.constant) config_from_newdirs() (in module coalispr.bedgraph_analyze.store) CONFNAM (in module coalispr.resources.constant) CONFPATH (in module coalispr.resources.constant) constant CONSTANT (in module coalispr.resources.constant) CONTEXT (in module coalispr.resources.constant) controls() (in module coalispr.bedgraph_analyze.experiment) convert_gff() (in module coalispr.resources.share.convert_gff3) convtab (in module coalispr.resources.share.genbank2gtf) CORB (in module coalispr.resources.constant) corbcntr (coalispr.bedgraph_analyze.bam_sample_counters.Sample_bin_counter attribute), [1] corbcount (coalispr.bedgraph_analyze.bam_sample_counters.Sample_bin_counter attribute) corbett COSEQ (in module coalispr.resources.constant) COU (in module coalispr.resources.constant) count_folder() (in module coalispr.bedgraph_analyze.process_bamdata) count_frames (coalispr.bedgraph_analyze.bam_keys_collators.Bam_samples_collator attribute) countbams() (in module coalispr.coalispr) CountPanelPlotter (class in coalispr.count_analyze.panel_plotters) coverage coverage() (in module coalispr.resources.profilehooks.profilehooks) (in module coalispr.resources.profilehooks.profilehooks_enable) CPPHFAC (in module coalispr.resources.constant) create_checkbtn() (coalispr.tk_gui.gui_widgets.opt2.Option_widget method) create_combo() (coalispr.tk_gui.gui_widgets.opt2.Option_widget method) create_comboE() (coalispr.tk_gui.gui_widgets.opt2.Option_widget method) create_entry() (coalispr.tk_gui.gui_widgets.opt2.Option_widget method) create_entry2() (coalispr.tk_gui.gui_widgets.opt2.Option_widget method) create_genom_indexes() (in module coalispr.bedgraph_analyze.genom) create_gtf() (in module coalispr.resources.share.sub_gtf) create_gtfs() (in module coalispr.resources.share.get_smallRNAs_and_targets) create_helpframe() (coalispr.tk_gui.gui_widgets.menu_main.Main_frame method) create_init_panel() (coalispr.tk_gui.gui_widgets.opt.Options_frame method) create_prog_frame() (coalispr.tk_gui.gui_widgets.menu_main.Command_frames method) create_runframe() (coalispr.tk_gui.gui_widgets.menu_main.Main_frame method) create_siRNA_GTF_line() (in module coalispr.resources.share.gtf_frm_tsv) CSFONTSZ (in module coalispr.resources.constant) csv current_widget (coalispr.tk_gui.gui_widgets.opt2.Subcommand_frame attribute), [1] custom_theme (coalispr.tk_gui.tk_coalispr.Coalispr_app attribute) CVAL1 (in module coalispr.resources.constant) CVAL2 (in module coalispr.resources.constant) CVAL3 (in module coalispr.resources.constant) CVAL4 (in module coalispr.resources.constant) CWD (in module coalispr.resources.constant) CYTO (in module coalispr.resources.constant)

D

DARKTHEME (in module coalispr.resources.constant) DATA (in module coalispr.resources.constant) DATASTOR (in module coalispr.resources.constant) DCOL (in module coalispr.resources.constant) DEFAULT_EMPTY_VALUE (in module coalispr.tk_gui.gui_constants) default_value (coalispr.tk_gui.gui_widgets.opt2.Option_widget attribute), [1] DENSE (in module coalispr.resources.constant) depletion kits DESCRIPTION (coalispr.tk_gui.gui_widgets.menu_main.Main_frame attribute) (in module coalispr.resources.constant) DETECTTHEME (in module coalispr.resources.constant) df (coalispr.bedgraph_analyze.genom.SegmentTrack attribute), [1] (coalispr.bedgraph_analyze.genom.Track attribute), [1] (coalispr.count_analyze.panel_plotters.BinPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.BrokenLengthPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.PanelPlotter attribute), [1]

discard DISCARD (in module coalispr.resources.constant) discarded() (in module coalispr.bedgraph_analyze.experiment) display_choices() (coalispr.resources.dialog.PresentDialog method) display_dialog() (coalispr.resources.dialog.PresentDialog method) DNAXTRA (in module coalispr.resources.constant) DNAXTRNAM (in module coalispr.resources.constant) DOCU (in module coalispr.tk_gui.gui_constants) dolegend (coalispr.count_analyze.panel_plotters.BinPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.BrokenLengthPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.LengthPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.PanelPlotter attribute), [1] doneon() (in module coalispr.resources.utilities) DPI (in module coalispr.resources.constant) drop_discarded() (in module coalispr.bedgraph_analyze.experiment) DWNLDS (in module coalispr.resources.constant)

E

edit_toolbar() (in module coalispr.resources.plot_utilities) enabled (coalispr.tk_gui.gui_widgets.opt2.Option_widget attribute), [1] (coalispr.tk_gui.gui_widgets.opt2.Subcommand_frame attribute) encoding (in module coalispr.bedgraph_analyze.compare) ENDRET (in module coalispr.resources.constant) epitope equals() (coalispr.resources.share.ncfasta2gtf.Gtfline method) errortext (coalispr.resources.dialog.PresentDialog attribute) EXCELL (in module coalispr.resources.constant) exclusive_arg_options (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1]

EXP (in module coalispr.resources.constant) EXPDISP (in module coalispr.resources.constant) EXPERIMENT (in module coalispr.resources.constant) EXPFILE (in module coalispr.resources.constant) EXPFILNAM (in module coalispr.resources.constant) EXPNAM (in module coalispr.resources.constant) EXPTXT (in module coalispr.resources.constant) extra exts (in module coalispr.resources.share.genbank2gtf) (in module coalispr.resources.share.gtf_frm_tsv) (in module coalispr.resources.share.ncfasta2gtf)

F

fasta FASTA (in module coalispr.resources.constant) fasta2gtf() (in module coalispr.resources.share.ncfasta2gtf) fastq fcie (coalispr.count_analyze.panel_plotters.BrokenLengthPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.CountPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.LengthPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.Log2CountPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.Log2RegionCountPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.RegionCountPanelPlotter attribute) (coalispr.resources.dialog.PresentDialog attribute), [1] FIELDFONTSIZE (in module coalispr.tk_gui.gui_constants) fig (coalispr.count_analyze.panel_plotters.PanelPlotter attribute) FIGCOL (in module coalispr.resources.constant) FIGDIR (in module coalispr.resources.constant) FIGDIRJPG (in module coalispr.resources.constant) FIGDIRPDF (in module coalispr.resources.constant) FIGDIRPNG (in module coalispr.resources.constant)

FIGDIRSVG (in module coalispr.resources.constant) FIGFORMAT (in module coalispr.resources.constant) FIGS (in module coalispr.resources.constant) figure (coalispr.count_analyze.panel_plotters.PanelPlotter attribute) FIGXLABEL (in module coalispr.resources.constant) FIGYLABEL (in module coalispr.resources.constant) FILEKEY (in module coalispr.resources.constant) filter_negative_from_reference() (in module coalispr.bedgraph_analyze.process_bedgraphs) filtered_referencetrack() (in module coalispr.bedgraph_analyze.references) Float64Index (class in coalispr.resources.numeric) floatformat() (coalispr.bedgraph_analyze.bam_keys_collators.Bam_samples_collator class method) FontManager (class in coalispr.tk_gui.customtkinter.font_manager) for_group() (in module coalispr.bedgraph_analyze.experiment) force (coalispr.bedgraph_analyze.process_bamdata.Bam_countprocessor attribute) format_ax (coalispr.count_analyze.panel_plotters.BrokenLengthPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.LengthPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.PanelPlotter attribute) FRACTION (in module coalispr.resources.constant) FRACTIONS (in module coalispr.resources.constant)

G

gap (coalispr.bedgraph_analyze.process_bamdata.Bam_countprocessor attribute) (coalispr.count_analyze.panel_plotters.PanelPlotter attribute), [1] gather_all_specific_regions() (in module coalispr.bedgraph_analyze.compare) gather_all_unspecific_regions() (in module coalispr.bedgraph_analyze.compare) genbank2gtf() (in module coalispr.resources.share.genbank2gtf) generate_frame_building_counters() (coalispr.bedgraph_analyze.bam_keys_collators.Bam_samples_collator class method) gentype (coalispr.resources.share.ncfasta2gtf.Gtfline attribute), [1] get_available_fonts() (in module coalispr.tk_gui.gui_utilities) get_bamfiles() (coalispr.bedgraph_analyze.process_bamdata.Bam_collector class method) get_categories_dict() (in module coalispr.bedgraph_analyze.collect_bedgraphs) get_coalispr_theme() (in module coalispr.tk_gui.gui_utilities) get_commands() (in module coalispr.coalispr) get_context() (in module coalispr.resources.plot_utilities) get_ctext() (coalispr.bedgraph_analyze.genom.Track method) get_descriptions() (in module coalispr.resources.cmd_parser) get_discard() (in module coalispr.bedgraph_analyze.experiment) get_experiment_name() (in module coalispr.resources.dialog) get_experiments() (in module coalispr.bedgraph_analyze.collect_bedgraphs) get_freq_frame() (in module coalispr.count_analyze.load_countfile) get_genom_indexes() (in module coalispr.bedgraph_analyze.genom) get_grplabels() (in module coalispr.bedgraph_analyze.experiment) get_GTF_comment() (in module coalispr.resources.share.gtf_frm_tsv) get_indexes() (in module coalispr.bedgraph_analyze.compare) get_input_widget() (coalispr.tk_gui.gui_widgets.opt2.Option_widget method) get_inputtotals() (in module coalispr.bedgraph_analyze.store) get_lengths() (in module coalispr.bedgraph_analyze.genom) get_mutant() (in module coalispr.bedgraph_analyze.experiment) get_negative() (in module coalispr.bedgraph_analyze.experiment) get_old_new_samplenames() (in module coalispr.resources.dialog) get_parser() (in module coalispr.coalispr) get_picks() (in module coalispr.bedgraph_analyze.experiment) get_positive() (in module coalispr.bedgraph_analyze.experiment) get_readlengths_frame() (in module coalispr.count_analyze.load_countfile) get_reference() (in module coalispr.bedgraph_analyze.experiment) get_region_count_frame() (coalispr.bedgraph_analyze.bam_keys_collators.Bam_samples_collator class method) get_region_frames() (coalispr.bedgraph_analyze.bam_keys_collators.Bam_samples_collator class method) get_region_pattern() (in module coalispr.resources.dialog) get_sample_counters() (coalispr.bedgraph_analyze.bam_sample_counters.Bam_sample_base_controller method) (coalispr.bedgraph_analyze.bam_sample_counters.Bam_sample_counter_controller method) (coalispr.bedgraph_analyze.bam_sample_counters.Bam_sample_region_counter_controller method)

get_segments() (coalispr.bedgraph_analyze.genom.Track method) get_skip() (in module coalispr.resources.utilities) get_string_info() (in module coalispr.resources.utilities) get_tsvpath() (in module coalispr.resources.utilities) get_unselected_folderpath() (in module coalispr.bedgraph_analyze.store) get_version() (in module coalispr.coalispr) get_ylabel() (in module coalispr.resources.utilities) goption() (in module coalispr.bedgraph_analyze.experiment) GRANUL (in module coalispr.resources.constant) GRID (in module coalispr.resources.constant) grid_column (coalispr.tk_gui.gui_widgets.opt2.Subcommand_frame attribute), [1] GRIDALPHA (in module coalispr.resources.constant) GRIDAXIS (in module coalispr.resources.constant) GRIDCOLOR (in module coalispr.resources.constant) GRIDSTYLE (in module coalispr.resources.constant) GRIDWHICH (in module coalispr.resources.constant) group (coalispr.count_analyze.panel_plotters.PanelPlotter attribute), [1] GROUP (in module coalispr.resources.constant) GROUPAVG (in module coalispr.resources.constant) groupcompare() (in module coalispr.coalispr) GTF GTFEXON (in module coalispr.resources.constant) GTFFEAT (in module coalispr.resources.constant) Gtfline (class in coalispr.resources.share.ncfasta2gtf) GTFREF (in module coalispr.resources.constant), [1] GTFREFNAM (in module coalispr.resources.constant) GTFS (in module coalispr.resources.constant) GTFSPEC (in module coalispr.resources.constant) GTFSPECNAM (in module coalispr.resources.constant) GTFtrack (class in coalispr.bedgraph_analyze.genom) GTFUNSP (in module coalispr.resources.constant) GTFUNSPNAM (in module coalispr.resources.constant) GTFUNXTNAM (in module coalispr.resources.constant) GTFUNXTR (in module coalispr.resources.constant) GTFXTRA (in module coalispr.resources.constant) GTFXTRANAM (in module coalispr.resources.constant) GUI

H

h99 (in module coalispr.resources.share.cols_from_csv_to_tab) h_tab (coalispr.tk_gui.gui_widgets.menu_main.Main_frame attribute) handle (coalispr.tk_gui.gui_widgets.opt2.Option_widget attribute), [1] has_been_counted() (in module coalispr.bedgraph_analyze.process_bamdata) has_discards() (in module coalispr.bedgraph_analyze.experiment) has_grouparg() (in module coalispr.bedgraph_analyze.experiment) has_redundant_muts() (in module coalispr.bedgraph_analyze.experiment) has_unselected() (in module coalispr.bedgraph_analyze.unselected) headers (in module coalispr.resources.share.gtf_frm_tsv)

HELP (coalispr.tk_gui.gui_widgets.menu_main.Main_frame attribute) hfac (coalispr.count_analyze.panel_plotters.LengthPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.PanelPlotter attribute), [1] (coalispr.count_analyze.panel_plotters.RegionCountPanelPlotter attribute) HI (in module coalispr.resources.constant) HIGHALPH (in module coalispr.resources.constant) HIGHLEG (in module coalispr.resources.constant) HIGHLINEW (in module coalispr.resources.constant) hold_frame (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1] HOME (in module coalispr.resources.constant)

I

idxnam (coalispr.bedgraph_analyze.bam_sample_counters.Sample_length_counter attribute) (coalispr.bedgraph_analyze.bam_sample_counters.Sample_multimap_counter attribute) immunoprecipitation in_venv() (in module coalispr.coalispr) INACTIVATE (in module coalispr.tk_gui.gui_constants) include_test() (in module coalispr.resources.utilities) IND (in module coalispr.bedgraph_analyze.bam_keys_collators) INFO (in module coalispr.tk_gui.gui_constants) info() (in module coalispr.coalispr) INFOREGS (in module coalispr.resources.constant) init() (in module coalispr.coalispr) init_counting() (coalispr.bedgraph_analyze.process_bamdata.Bam_countprocessor class method) init_font_manager() (coalispr.tk_gui.customtkinter.font_manager.FontManager class method) init_panel (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute)

init_sns() (in module coalispr.resources.plot_utilities) INMAPCOLL (in module coalispr.resources.constant) INMAPUNCOLL (in module coalispr.resources.constant) input (coalispr.tk_gui.gui_widgets.opt2.Option_widget attribute), [1] INPUTRCS (in module coalispr.resources.constant) Int64Index (class in coalispr.resources.numeric) IntegerIndex (class in coalispr.resources.numeric) INTR (in module coalispr.resources.constant) INTSTEP (in module coalispr.resources.constant) IP is_all_zero() (in module coalispr.resources.utilities) is_one_of_list() (coalispr.tk_gui.gui_widgets.opt2.Option_widget method) is_one_of_list_ (coalispr.tk_gui.gui_widgets.opt2.Option_widget attribute), [1] item (coalispr.resources.dialog.PresentDialog attribute), [1]

J

jec21 (in module coalispr.resources.share.cols_from_csv_to_tab) joinall() (in module coalispr.resources.utilities)

joiner() (in module coalispr.resources.utilities) JPG (in module coalispr.resources.constant)

K

key (coalispr.bedgraph_analyze.bam_sample_counters.Bam_sample_base_controller attribute), [1] (coalispr.bedgraph_analyze.bam_sample_counters.Bam_sample_counter_controller attribute) (coalispr.bedgraph_analyze.bam_sample_counters.Bam_sample_region_counter_controller attribute) (coalispr.bedgraph_analyze.bam_sample_counters.Sample_counter attribute), [1] (coalispr.tk_gui.gui_widgets.opt2.Option_widget attribute)

keycntr (coalispr.bedgraph_analyze.bam_sample_counters.Sample_region_length_counter attribute) keys (coalispr.bedgraph_analyze.process_bamdata.Bam_countprocessor attribute) keys_counted_libs() (coalispr.bedgraph_analyze.process_bamdata.Bam_collector class method) kind (coalispr.bedgraph_analyze.genom.GTFtrack attribute), [1] (coalispr.bedgraph_analyze.process_bamdata.Bam_countprocessor attribute)

L

label (coalispr.bedgraph_analyze.bam_sample_counters.Sample_counter attribute), [1] label0 (coalispr.tk_gui.gui_widgets.opt2.Option_widget attribute), [1] label1 (coalispr.tk_gui.gui_widgets.opt2.Option_widget attribute), [1] label_frame() (in module coalispr.bedgraph_analyze.collect_bedgraphs) labframe (coalispr.tk_gui.gui_widgets.opt2.Subcommand_frame attribute), [1] LEGNCOL (in module coalispr.resources.constant) LEN (in module coalispr.resources.constant) LENCDNA (in module coalispr.resources.constant) LENCNTRS (in module coalispr.resources.constant) LENCNTS (in module coalispr.resources.constant) LENCOUNTS (in module coalispr.resources.constant) LENGAP (in module coalispr.resources.constant) LengthPanelPlotter (class in coalispr.count_analyze.panel_plotters) LENGTHSFILE (in module coalispr.resources.constant) LENGTHSNAM (in module coalispr.resources.constant) LENMER (in module coalispr.resources.constant) LENREAD (in module coalispr.resources.constant) lens (coalispr.count_analyze.panel_plotters.PanelPlotter attribute), [1] LENXTRA (in module coalispr.resources.constant) LENXTRAFILE (in module coalispr.resources.constant) less_xlabels() (in module coalispr.resources.plot_utilities) LIBCNTS (in module coalispr.resources.constant) LIBR (in module coalispr.resources.constant) lineobjects (coalispr.resources.share.ncfasta2gtf.Gtfline attribute) LINEW (in module coalispr.resources.constant) LINLIM (in module coalispr.resources.constant) linux_font_path (coalispr.tk_gui.customtkinter.font_manager.FontManager attribute) load_bin_table_perc() (in module coalispr.count_analyze.load_countfile) load_command() (coalispr.tk_gui.gui_widgets.menu_main.Cli_menu method) load_count_table() (in module coalispr.count_analyze.load_countfile) load_file() (in module coalispr.resources.share.cols_from_csv_to_tab) load_font() (coalispr.tk_gui.customtkinter.font_manager.FontManager class method) load_lengths_table_perc() (in module coalispr.count_analyze.load_countfile) load_list() (in module coalispr.resources.share.cols_from_csv_to_tab) log2_ax (coalispr.count_analyze.panel_plotters.CountPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.Log2CountPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.Log2RegionCountPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.RegionCountPanelPlotter attribute)

LOG2BG (in module coalispr.resources.constant) LOG2BGTST (in module coalispr.resources.constant) Log2CountPanelPlotter (class in coalispr.count_analyze.panel_plotters) Log2RegionCountPanelPlotter (class in coalispr.count_analyze.panel_plotters) LOGFIL (in module coalispr.resources.constant) LOGFILNAM (in module coalispr.resources.constant) logger (in module coalispr.bedgraph_analyze.bam_keys_collators) (in module coalispr.bedgraph_analyze.bam_sample_counters) (in module coalispr.bedgraph_analyze.bedgraph_plots) (in module coalispr.bedgraph_analyze.collect_bedgraphs) (in module coalispr.bedgraph_analyze.compare) (in module coalispr.bedgraph_analyze.genom) (in module coalispr.bedgraph_analyze.info_plots) (in module coalispr.bedgraph_analyze.process_bamdata) (in module coalispr.bedgraph_analyze.process_bedgraphs) (in module coalispr.bedgraph_analyze.references) (in module coalispr.bedgraph_analyze.store) (in module coalispr.bedgraph_analyze.unselected) (in module coalispr.count_analyze.annot) (in module coalispr.count_analyze.countfile_plots) (in module coalispr.count_analyze.groupcompare_plots) (in module coalispr.count_analyze.load_countfile) (in module coalispr.count_analyze.panel_plotters) (in module coalispr.count_analyze.regioncount_plots) (in module coalispr.resources.constant_in.make_constant) (in module coalispr.resources.dialog) (in module coalispr.resources.plot_utilities) (in module coalispr.resources.utilities) (in module coalispr.tk_gui.gui_utilities) (in module coalispr.tk_gui.gui_widgets.menu_main) (in module coalispr.tk_gui.tk_coalispr) LOGLIM (in module coalispr.resources.constant) LOGMAX (in module coalispr.resources.constant) LOGO (in module coalispr.tk_gui.gui_constants) LOGS (in module coalispr.resources.constant) LOWLEG (in module coalispr.resources.constant) LOWR (in module coalispr.resources.constant) LPPHFAC (in module coalispr.resources.constant) LWIDTH (in module coalispr.tk_gui.gui_constants)

M

main (coalispr.tk_gui.tk_coalispr.Coalispr_app attribute) main() (in module coalispr.coalispr) (in module coalispr.resources.constant_in.make_constant) (in module coalispr.resources.share.clean_fasta) (in module coalispr.resources.share.cols_from_csv_to_tab) (in module coalispr.resources.share.convert_gff3) (in module coalispr.resources.share.convert_plusmin_bedgraph_to_plusplus) (in module coalispr.resources.share.genbank2gtf) (in module coalispr.resources.share.get_smallRNAs_and_targets) (in module coalispr.resources.share.gtf_frm_tsv) (in module coalispr.resources.share.ncfasta2gtf) (in module coalispr.resources.share.no_empty_fa) (in module coalispr.resources.share.reduce_gtf) (in module coalispr.resources.share.revseq) (in module coalispr.resources.share.sub_gtf) (in module coalispr.tk_gui.tk_coalispr) Main_frame (class in coalispr.tk_gui.gui_widgets.menu_main) maincut (coalispr.bedgraph_analyze.process_bamdata.Bam_countprocessor attribute) make_cigarcheck() (coalispr.bedgraph_analyze.process_bamdata.Read_checker class method) make_constant() (in module coalispr.resources.constant_in.make_constant) make_parser() (in module coalispr.resources.cmd_parser) master (coalispr.tk_gui.gui_widgets.menu_main.Command_frames attribute) (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1] MAXGAP (in module coalispr.resources.constant) MAXMM (in module coalispr.resources.constant) MAXROW (in module coalispr.resources.constant) MCOL (in module coalispr.resources.constant) MEAN (in module coalispr.resources.constant) MEDIAN (in module coalispr.resources.constant) MEMBR (in module coalispr.resources.constant) menu (coalispr.tk_gui.tk_coalispr.Coalispr_app attribute) MENUFONTSIZE (in module coalispr.tk_gui.gui_constants) merg() (in module coalispr.resources.utilities) merge_reference() (in module coalispr.bedgraph_analyze.process_bedgraphs) merge_sets() (in module coalispr.bedgraph_analyze.process_bedgraphs) merge_unsel() (in module coalispr.bedgraph_analyze.unselected) METHCOL (in module coalispr.resources.constant) METHOD (in module coalispr.resources.constant) METHODS (in module coalispr.resources.constant) MI (in module coalispr.resources.constant) MINGAP (in module coalispr.resources.constant) MININTRON (in module coalispr.resources.constant) MINUS (in module coalispr.resources.constant) MINUSIN (in module coalispr.resources.constant) miRNA MIRNAPKBUF (in module coalispr.resources.constant) MITOCH (in module coalispr.resources.constant) mixed_groups() (in module coalispr.bedgraph_analyze.experiment) MMAPCNTRS (in module coalispr.resources.constant) mmapper_dict (coalispr.bedgraph_analyze.bam_keys_collators.Bam_samples_collator attribute) mmappers (coalispr.bedgraph_analyze.bam_sample_counters.Bam_sample_base_controller attribute), [1] (coalispr.bedgraph_analyze.bam_sample_counters.Bam_sample_counter_controller attribute), [1] MMAPPERS (in module coalispr.bedgraph_analyze.bam_keys_collators) module coalispr coalispr.bedgraph_analyze coalispr.bedgraph_analyze.bam_keys_collators coalispr.bedgraph_analyze.bam_sample_counters coalispr.bedgraph_analyze.bedgraph_plots coalispr.bedgraph_analyze.collect_bedgraphs coalispr.bedgraph_analyze.compare coalispr.bedgraph_analyze.experiment coalispr.bedgraph_analyze.genom coalispr.bedgraph_analyze.info_plots coalispr.bedgraph_analyze.process_bamdata coalispr.bedgraph_analyze.process_bedgraphs coalispr.bedgraph_analyze.references coalispr.bedgraph_analyze.store coalispr.bedgraph_analyze.unselected coalispr.coalispr coalispr.count_analyze coalispr.count_analyze.annot coalispr.count_analyze.countfile_plots coalispr.count_analyze.filter_data coalispr.count_analyze.groupcompare_plots coalispr.count_analyze.load_countfile coalispr.count_analyze.panel_plotters coalispr.count_analyze.regioncount_plots coalispr.resources coalispr.resources.cmd_parser coalispr.resources.constant coalispr.resources.constant_in coalispr.resources.constant_in.make_constant coalispr.resources.dialog coalispr.resources.numeric coalispr.resources.plot_utilities coalispr.resources.profilehooks coalispr.resources.profilehooks.profilehooks coalispr.resources.profilehooks.profilehooks_enable coalispr.resources.share coalispr.resources.share.clean_fasta coalispr.resources.share.cols_from_csv_to_tab coalispr.resources.share.convert_gff3 coalispr.resources.share.convert_plusmin_bedgraph_to_plusplus coalispr.resources.share.genbank2gtf coalispr.resources.share.get_smallRNAs_and_targets coalispr.resources.share.gtf_frm_tsv coalispr.resources.share.ncfasta2gtf coalispr.resources.share.no_empty_fa coalispr.resources.share.reduce_gtf coalispr.resources.share.revseq coalispr.resources.share.sub_gtf coalispr.resources.utilities coalispr.tk_gui coalispr.tk_gui.customtkinter coalispr.tk_gui.customtkinter.font_manager coalispr.tk_gui.gui_constants coalispr.tk_gui.gui_utilities coalispr.tk_gui.gui_widgets coalispr.tk_gui.gui_widgets.menu_main coalispr.tk_gui.gui_widgets.opt coalispr.tk_gui.gui_widgets.opt2 coalispr.tk_gui.tk_coalispr

mouse (in module coalispr.resources.share.cols_from_csv_to_tab) MPLDEBUG (in module coalispr.resources.constant) mRNA msg (coalispr.resources.dialog.PresentDialog attribute) msg1 (coalispr.resources.dialog.PresentDialog attribute) msg2 (coalispr.resources.dialog.PresentDialog attribute) MULMAP (in module coalispr.resources.constant) MULMAPCOLL (in module coalispr.resources.constant) MULMAPUNCOLL (in module coalispr.resources.constant) multimapper MUNR (in module coalispr.resources.constant) munrcntr (coalispr.bedgraph_analyze.bam_sample_counters.Sample_bin_counter attribute), [1] munrcount (coalispr.bedgraph_analyze.bam_sample_counters.Sample_bin_counter attribute) munro mutant MUTANT (in module coalispr.resources.constant) mutant() (in module coalispr.bedgraph_analyze.experiment) mutant_groups() (in module coalispr.bedgraph_analyze.experiment) MUTANTS (in module coalispr.resources.constant) MUTGROUPS (in module coalispr.resources.constant) MUTNO (in module coalispr.resources.constant)

N

name (in module coalispr) (in module coalispr.bedgraph_analyze) (in module coalispr.count_analyze) (in module coalispr.resources) (in module coalispr.resources.constant_in) (in module coalispr.resources.profilehooks) (in module coalispr.resources.share) (in module coalispr.tk_gui) (in module coalispr.tk_gui.customtkinter) (in module coalispr.tk_gui.gui_widgets) nams (coalispr.count_analyze.panel_plotters.PanelPlotter attribute), [1] NCOL (in module coalispr.resources.constant) negative control negative() (in module coalispr.bedgraph_analyze.experiment) NEGCTL (in module coalispr.resources.constant) NH (in module coalispr.resources.constant) NM (in module coalispr.resources.constant) NMD

no_titles() (in module coalispr.resources.plot_utilities) NOCHOICE (in module coalispr.resources.constant) nodiscards_keys (coalispr.bedgraph_analyze.process_bamdata.Bam_collector attribute), [1] noise nomis (coalispr.bedgraph_analyze.process_bamdata.Bam_countprocessor attribute) (coalispr.bedgraph_analyze.process_bamdata.Read_checker attribute), [1] NONCAPT (in module coalispr.resources.constant) not_keycntr (coalispr.bedgraph_analyze.bam_sample_counters.Sample_skip_counter attribute) NOTAGIP (in module coalispr.resources.constant) notcntr (coalispr.bedgraph_analyze.bam_sample_counters.Sample_skip_counter attribute) notcount (coalispr.bedgraph_analyze.bam_sample_counters.Sample_skip_counter attribute) notfram (coalispr.bedgraph_analyze.bam_sample_counters.Sample_skip_counter attribute) NRMISM (in module coalispr.resources.constant) nt NUCL (in module coalispr.resources.constant) NUCLEO (in module coalispr.resources.constant) num_counted_libs() (coalispr.bedgraph_analyze.process_bamdata.Bam_collector class method) numbers (coalispr.count_analyze.panel_plotters.PanelPlotter attribute), [1] NumericIndex (class in coalispr.resources.numeric)

O

ok_read() (coalispr.bedgraph_analyze.process_bamdata.Read_checker class method) ok_strand() (coalispr.bedgraph_analyze.process_bamdata.Read_checker class method) okintrons (coalispr.bedgraph_analyze.process_bamdata.Read_checker attribute), [1] on_closing() (coalispr.tk_gui.tk_coalispr.Coalispr_app method) on_invalid() (coalispr.tk_gui.gui_widgets.opt2.Option_widget method) one_of_destinations (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1]

open_cmd (coalispr.tk_gui.tk_coalispr.Coalispr_app attribute) Option_widget (class in coalispr.tk_gui.gui_widgets.opt2) Options_frame (class in coalispr.tk_gui.gui_widgets.opt) OTHR (in module coalispr.resources.constant) othr() (in module coalispr.bedgraph_analyze.experiment) OUTPATH (in module coalispr.resources.constant) OUTPUTS (in module coalispr.resources.constant)

P

p (in module coalispr.resources.constant) (in module coalispr.tk_gui.gui_constants) (in module coalispr.tk_gui.gui_utilities) (in module coalispr.tk_gui.tk_coalispr) P2TDELIM (in module coalispr.resources.constant) PALETTE (in module coalispr.resources.constant) PanelPlotter (class in coalispr.count_analyze.panel_plotters) parent (coalispr.tk_gui.gui_widgets.menu_main.Cli_menu attribute), [1] (coalispr.tk_gui.gui_widgets.opt2.Option_widget attribute), [1] parse_open() (in module coalispr.tk_gui.tk_coalispr) pattern (coalispr.resources.dialog.PresentDialog attribute), [1] PCKG (in module coalispr.tk_gui.gui_constants) PCR PDF (in module coalispr.resources.constant) PE per_confirm (coalispr.resources.dialog.PresentDialog attribute), [1] PERC (in module coalispr.resources.constant) percentaged() (in module coalispr.resources.utilities) pickle_from_backup_tsv() (in module coalispr.bedgraph_analyze.store) pkl PKL2TSV (in module coalispr.resources.constant) PL (in module coalispr.resources.constant) plot_chrset() (in module coalispr.bedgraph_analyze.bedgraph_plots) plot_panels() (coalispr.count_analyze.panel_plotters.PanelPlotter method) plot_regioncounts() (in module coalispr.count_analyze.regioncount_plots) plot_regionlengths() (in module coalispr.count_analyze.regioncount_plots) PLOTALL (in module coalispr.resources.constant) PLOTFREQ (in module coalispr.resources.constant) PLOTINTRLEN (in module coalispr.resources.constant) PLOTLEN (in module coalispr.resources.constant) PLOTLIB (in module coalispr.resources.constant) PLOTMEAN (in module coalispr.resources.constant)

PLOTMEDIAN (in module coalispr.resources.constant) PLOTMMAP (in module coalispr.resources.constant) PLOTPERC (in module coalispr.resources.constant) PLOTRAW (in module coalispr.resources.constant) PLOTSPEC (in module coalispr.resources.constant) PLOTSTRT (in module coalispr.resources.constant) PLOTUNSP (in module coalispr.resources.constant) PLUS (in module coalispr.resources.constant) PLUSIN (in module coalispr.resources.constant) png PNG (in module coalispr.resources.constant) POSCTL (in module coalispr.resources.constant) positive control positive() (in module coalispr.bedgraph_analyze.experiment) posslabels (in module coalispr.count_analyze.regioncount_plots) prefix (in module coalispr.resources.share.gtf_frm_tsv) PresentDialog (class in coalispr.resources.dialog) PRGNAM (in module coalispr.resources.constant) print_memory_usage_merged() (in module coalispr.bedgraph_analyze.store) printme() (coalispr.resources.share.ncfasta2gtf.Gtfline method) process_bam_files() (in module coalispr.bedgraph_analyze.process_bamdata) process_bamfile() (coalispr.bedgraph_analyze.process_bamdata.Bam_countprocessor class method) process_graphs() (in module coalispr.bedgraph_analyze.process_bedgraphs) process_reads_for_region() (in module coalispr.bedgraph_analyze.process_bamdata) process_reference() (in module coalispr.bedgraph_analyze.process_bedgraphs) process_unselected() (in module coalispr.bedgraph_analyze.unselected) profile() (in module coalispr.resources.profilehooks.profilehooks) (in module coalispr.resources.profilehooks.profilehooks_enable) prog (in module coalispr.resources.cmd_parser) PROG_DESCRIPTION (in module coalispr.tk_gui.gui_constants) PROPR (in module coalispr.resources.constant) Python

R

r_tab (coalispr.tk_gui.gui_widgets.menu_main.Main_frame attribute) RBP RCOL (in module coalispr.resources.constant) Read_checker (class in coalispr.bedgraph_analyze.process_bamdata) READCOUNTS (in module coalispr.resources.constant) READDENS (in module coalispr.resources.constant) recombine_controllers() (coalispr.bedgraph_analyze.bam_keys_collators.Bam_samples_collator class method) reduce_gtf() (in module coalispr.resources.share.reduce_gtf) ref_at_clickpoint() (in module coalispr.bedgraph_analyze.genom) ref_in_segment() (in module coalispr.bedgraph_analyze.genom) REFDIR (in module coalispr.resources.constant) reference REFERENCE (in module coalispr.resources.constant) reference() (in module coalispr.bedgraph_analyze.experiment) referencetrack() (in module coalispr.bedgraph_analyze.references) REFNDIRLEVEL (in module coalispr.resources.constant) REFS (in module coalispr.resources.constant) REGCNTRS (in module coalispr.resources.constant) REGCNTS (in module coalispr.resources.constant) REGI (in module coalispr.resources.constant) region (coalispr.bedgraph_analyze.bam_sample_counters.Bam_sample_region_counter_controller attribute), [1] (coalispr.bedgraph_analyze.process_bamdata.Bam_countprocessor attribute) region() (in module coalispr.coalispr) RegionCountPanelPlotter (class in coalispr.count_analyze.panel_plotters) REGS (in module coalispr.resources.constant) remove_odds() (in module coalispr.resources.utilities) rename_in_count_tsv() (in module coalispr.bedgraph_analyze.store) rename_in_data_tsv() (in module coalispr.bedgraph_analyze.store) rename_in_expfile() (in module coalispr.bedgraph_analyze.store) rename_unselected() (in module coalispr.bedgraph_analyze.store) repair REPAIR (in module coalispr.resources.constant)

replace_dot() (in module coalispr.resources.utilities) replacelist() (in module coalispr.resources.utilities) replacelist_list() (in module coalispr.resources.utilities) report_skipped() (coalispr.bedgraph_analyze.bam_sample_counters.Bam_sample_base_controller method) (coalispr.bedgraph_analyze.bam_sample_counters.Sample_skip_counter method) REPS (in module coalispr.resources.constant) reset_current_combo_widget() (coalispr.tk_gui.gui_widgets.opt2.Subcommand_frame method) resizable (coalispr.tk_gui.tk_coalispr.Coalispr_app attribute) REST (in module coalispr.resources.constant) rest_commands (coalispr.tk_gui.gui_widgets.menu_main.Command_frames attribute) restart() (coalispr.tk_gui.tk_coalispr.Coalispr_app method) restart_cmd (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1] restart_on_submit (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1] retrieve_all_chr_regions_from_tsv() (in module coalispr.bedgraph_analyze.genom) retrieve_chr_regions_from_tsv() (in module coalispr.bedgraph_analyze.genom) retrieve_merged() (in module coalispr.bedgraph_analyze.store) retrieve_merged_reference() (in module coalispr.bedgraph_analyze.references) retrieve_merged_unselected() (in module coalispr.bedgraph_analyze.store) retrieve_processed_files() (in module coalispr.bedgraph_analyze.store) revseq() (in module coalispr.resources.share.revseq) RIP RIP1 (in module coalispr.resources.constant) RIP2 (in module coalispr.resources.constant) RLENCOUNTS (in module coalispr.resources.constant) rlessx (coalispr.count_analyze.panel_plotters.LengthPanelPlotter attribute) RNA-seq RNAi RPM rRFs rRNA run_all_bamcount_processes() (coalispr.bedgraph_analyze.process_bamdata.Bam_countprocessor class method) run_coalispr() (in module coalispr.coalispr) run_region_count_processes() (coalispr.bedgraph_analyze.process_bamdata.Bam_countprocessor class method)

S

SAMBAM (in module coalispr.resources.constant) SAMPLE (in module coalispr.resources.constant) Sample_bin_counter (class in coalispr.bedgraph_analyze.bam_sample_counters) sample_controllers (coalispr.bedgraph_analyze.bam_keys_collators.Bam_samples_collator attribute) Sample_counter (class in coalispr.bedgraph_analyze.bam_sample_counters) Sample_length_counter (class in coalispr.bedgraph_analyze.bam_sample_counters) Sample_multimap_counter (class in coalispr.bedgraph_analyze.bam_sample_counters) Sample_region_length_counter (class in coalispr.bedgraph_analyze.bam_sample_counters) Sample_skip_counter (class in coalispr.bedgraph_analyze.bam_sample_counters) sampls (coalispr.count_analyze.panel_plotters.PanelPlotter attribute), [1] savdir (coalispr.count_analyze.panel_plotters.BinPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.CountPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.LengthPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.Log2CountPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.Log2RegionCountPanelPlotter attribute) (coalispr.count_analyze.panel_plotters.PanelPlotter attribute), [1] (coalispr.count_analyze.panel_plotters.RegionCountPanelPlotter attribute) save_average_table() (in module coalispr.bedgraph_analyze.store) save_bincounters_to_tsv() (coalispr.bedgraph_analyze.bam_keys_collators.Bam_samples_collator class method) save_frame_with_region_lengthcounts_to_tsv() (coalispr.bedgraph_analyze.bam_keys_collators.Bam_samples_collator class method) save_length_counters_to_tsv() (coalispr.bedgraph_analyze.bam_keys_collators.Bam_samples_collator class method) save_output_as() (in module coalispr.resources.plot_utilities) save_region_counters_to_tsv() (coalispr.bedgraph_analyze.bam_keys_collators.Bam_samples_collator class method) save_skip_counters_to_tsv() (coalispr.bedgraph_analyze.bam_keys_collators.Bam_samples_collator class method) save_to_tsv() (coalispr.bedgraph_analyze.bam_keys_collators.Bam_samples_collator class method) SAVEBAM (in module coalispr.resources.constant) savedirect (coalispr.count_analyze.panel_plotters.PanelPlotter attribute) SAVEIN (in module coalispr.resources.constant) SAVEJPG (in module coalispr.resources.constant) SAVEPDF (in module coalispr.resources.constant) SAVEPNG (in module coalispr.resources.constant) SAVESVG (in module coalispr.resources.constant) SAVETSV (in module coalispr.resources.constant) SCOL (in module coalispr.resources.constant) scroll_canvas (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1] scroll_height (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1] scrollable_frame (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1] SCROLLH (in module coalispr.tk_gui.gui_constants) SE SegmentTrack (class in coalispr.bedgraph_analyze.genom) segs (coalispr.bedgraph_analyze.process_bamdata.Bam_countprocessor attribute) SEGSUM (in module coalispr.resources.constant) select_from() (in module coalispr.resources.dialog) selectbam (coalispr.bedgraph_analyze.process_bamdata.Bam_countprocessor attribute) selected_item (coalispr.tk_gui.gui_widgets.menu_main.Cli_menu attribute), [1] seq_id seqend (coalispr.resources.share.ncfasta2gtf.Gtfline attribute), [1] seqid (coalispr.resources.share.ncfasta2gtf.Gtfline attribute), [1] seqstart (coalispr.resources.share.ncfasta2gtf.Gtfline attribute), [1] set_axes() (in module coalispr.resources.plot_utilities) set_bincounts() (coalispr.bedgraph_analyze.bam_sample_counters.Bam_sample_base_controller method) (coalispr.bedgraph_analyze.bam_sample_counters.Sample_bin_counter method) (coalispr.bedgraph_analyze.bam_sample_counters.Sample_counter method) (coalispr.bedgraph_analyze.bam_sample_counters.Sample_region_length_counter method) (coalispr.bedgraph_analyze.bam_sample_counters.Sample_skip_counter method) set_command_field() (coalispr.tk_gui.gui_widgets.opt.Options_frame method) set_fonts() (coalispr.tk_gui.tk_coalispr.Coalispr_app method) set_help_fields() (coalispr.tk_gui.gui_widgets.menu_main.Main_frame method) set_loaded_command() (coalispr.tk_gui.tk_coalispr.Coalispr_app method) set_run_fields() (coalispr.tk_gui.gui_widgets.menu_main.Main_frame method) set_sample_controllers() (coalispr.bedgraph_analyze.bam_keys_collators.Bam_samples_collator class method) set_style() (coalispr.tk_gui.tk_coalispr.Coalispr_app method) set_subcommand() (coalispr.tk_gui.gui_widgets.opt2.Subcommand_frame method) SETBASE (in module coalispr.resources.constant) setexp() (in module coalispr.coalispr) SGFONTSZ (in module coalispr.resources.constant) SGHEIGHT (in module coalispr.resources.constant) SGWIDTH (in module coalispr.resources.constant) SHARED (in module coalispr.resources.constant)

SHIPPEDFONT (in module coalispr.tk_gui.gui_constants) SHORT (in module coalispr.resources.constant) show_chr() (in module coalispr.bedgraph_analyze.process_bedgraphs) show_mapped_vs_unmapped() (in module coalispr.bedgraph_analyze.info_plots) show_regions_vs_settings() (in module coalispr.bedgraph_analyze.info_plots) show_specific_chr() (in module coalispr.bedgraph_analyze.process_bedgraphs) show_unspecific_chr() (in module coalispr.bedgraph_analyze.process_bedgraphs) showcounts() (in module coalispr.coalispr) SHOWDISC (in module coalispr.resources.constant) showgraphs() (in module coalispr.coalispr) SHWABT (in module coalispr.tk_gui.gui_constants) siRNA size (coalispr.tk_gui.tk_coalispr.Coalispr_app attribute) sizegrip (coalispr.tk_gui.tk_coalispr.Coalispr_app attribute) sizer_dict (coalispr.bedgraph_analyze.bam_keys_collators.Bam_samples_collator attribute) sizers (coalispr.bedgraph_analyze.bam_sample_counters.Bam_sample_base_controller attribute), [1] (coalispr.bedgraph_analyze.bam_sample_counters.Bam_sample_counter_controller attribute), [1] (coalispr.bedgraph_analyze.bam_sample_counters.Bam_sample_region_counter_controller attribute), [1] SIZERS (in module coalispr.bedgraph_analyze.bam_keys_collators) SKIP (coalispr.resources.dialog.PresentDialog attribute) (in module coalispr.resources.constant) skip_count() (coalispr.bedgraph_analyze.bam_sample_counters.Bam_sample_base_controller method) (coalispr.bedgraph_analyze.bam_sample_counters.Sample_skip_counter method) skip_duplicates() (coalispr.resources.share.ncfasta2gtf.Gtfline method) SKIPINT (in module coalispr.resources.constant) smallest2chroms() (in module coalispr.bedgraph_analyze.genom) smear SNSFNTFAM (in module coalispr.resources.constant) SNSFNTSZ (in module coalispr.resources.constant) soft-clipping sort_and_remove_duplicates() (coalispr.resources.share.ncfasta2gtf.Gtfline method) source (coalispr.resources.share.ncfasta2gtf.Gtfline attribute), [1] SOURCE (in module coalispr.resources.constant) SPAN (in module coalispr.resources.constant) specific SPECIFIC (in module coalispr.resources.constant) specific() (in module coalispr.bedgraph_analyze.compare) specified split_readlengths_index() (in module coalispr.count_analyze.load_countfile) SRCDIR (in module coalispr.resources.constant) SRCE (in module coalispr.tk_gui.gui_constants) SRCFLDR (in module coalispr.resources.constant) SRCNDIRLEVEL (in module coalispr.resources.constant) SRCPRGNAM (in module coalispr.resources.constant) start_logging() (in module coalispr.coalispr) STARV (in module coalispr.resources.constant) STEM (in module coalispr.resources.constant) stop (coalispr.resources.dialog.PresentDialog attribute) stopmsg (coalispr.resources.dialog.PresentDialog attribute) store_chromosome_data() (in module coalispr.bedgraph_analyze.store) store_chromosome_data_as_tsv() (in module coalispr.bedgraph_analyze.store) store_processed_chrindexes() (in module coalispr.bedgraph_analyze.store) storedata() (in module coalispr.coalispr) STOREPATH (in module coalispr.resources.constant) STOREPICKLE (in module coalispr.resources.constant) strand (coalispr.bedgraph_analyze.genom.GTFtrack attribute), [1] (coalispr.bedgraph_analyze.process_bamdata.Bam_countprocessor attribute) (coalispr.resources.share.ncfasta2gtf.Gtfline attribute), [1] STRTCMD (in module coalispr.tk_gui.gui_constants) subcom_var (coalispr.tk_gui.gui_widgets.opt2.Subcommand_frame attribute), [1] SUBCOMMAND (in module coalispr.tk_gui.gui_constants) Subcommand_frame (class in coalispr.tk_gui.gui_widgets.opt2) subcommands_info (coalispr.tk_gui.gui_widgets.opt2.Subcommand_frame attribute) subcoms (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1] SUBFIGS (in module coalispr.resources.constant) submitbutton_clicked() (coalispr.tk_gui.gui_widgets.opt.Options_frame method) submittip (coalispr.tk_gui.gui_widgets.opt.Options_frame attribute), [1] suggest_storepath() (in module coalispr.resources.dialog) svg SVG (in module coalispr.resources.constant)

T

TAB_LABELS (coalispr.tk_gui.gui_widgets.menu_main.Main_frame attribute) tag (coalispr.bedgraph_analyze.process_bamdata.Bam_collector attribute), [1] TAG (in module coalispr.resources.constant) tagBam (coalispr.bedgraph_analyze.process_bamdata.Bam_countprocessor attribute) TAGBAM (in module coalispr.resources.constant) TAGCOLL (in module coalispr.resources.constant) tagSeg (coalispr.bedgraph_analyze.process_bamdata.Bam_countprocessor attribute) TAGSEG (in module coalispr.resources.constant) TAGUNCOLL (in module coalispr.resources.constant) technical replicate TEST (coalispr.bedgraph_analyze.process_bamdata.Bam_countprocessor attribute) (in module coalispr.count_analyze.annot) (in module coalispr.resources.utilities) test() (in module coalispr.coalispr) test_intervals() (in module coalispr.bedgraph_analyze.compare) textlist() (coalispr.bedgraph_analyze.genom.GTFtrack method) (coalispr.bedgraph_analyze.genom.SegmentTrack method) (coalispr.bedgraph_analyze.genom.Track method) THEME_DARK (in module coalispr.tk_gui.gui_constants) THEME_LIGHT (in module coalispr.tk_gui.gui_constants) THISALPH (in module coalispr.resources.constant) thisfile (in module coalispr.tk_gui.tk_coalispr) thisfunc() (in module coalispr.resources.utilities) timecall() (in module coalispr.resources.profilehooks.profilehooks) (in module coalispr.resources.profilehooks.profilehooks_enable) timer() (in module coalispr.resources.utilities) tip_text (coalispr.tk_gui.gui_widgets.opt2.Option_widget attribute), [1]

titels (coalispr.count_analyze.panel_plotters.PanelPlotter attribute) title (coalispr.tk_gui.tk_coalispr.Coalispr_app attribute) titles (coalispr.count_analyze.panel_plotters.PanelPlotter attribute) TKFONTSIZE (in module coalispr.tk_gui.gui_constants) TKHEIGHT (in module coalispr.tk_gui.gui_constants) TKOFFSET (in module coalispr.tk_gui.gui_constants) TKRESIZABLE (in module coalispr.tk_gui.gui_constants) TKWIDTH (in module coalispr.tk_gui.gui_constants) TMP (in module coalispr.resources.constant) TOTAL (in module coalispr.resources.constant) total_raw_counts() (in module coalispr.bedgraph_analyze.process_bamdata) TOTALS (in module coalispr.resources.constant) TOTINPUT (in module coalispr.resources.constant) Track (class in coalispr.bedgraph_analyze.genom) TRACKLABEL (in module coalispr.resources.constant) tresh (coalispr.bedgraph_analyze.process_bamdata.Bam_countprocessor attribute) tRNA TRSHLD (in module coalispr.resources.constant) try_input() (coalispr.resources.dialog.PresentDialog method) TSTREGIONS (in module coalispr.resources.constant) tsv TSV (in module coalispr.resources.constant) tsv2gtf() (in module coalispr.resources.share.gtf_frm_tsv) TSV2PKL (in module coalispr.resources.constant) tsvpath (coalispr.bedgraph_analyze.process_bamdata.Bam_countprocessor attribute) tutorials (in module coalispr.resources.share.cols_from_csv_to_tab) TXTALIAS (in module coalispr.resources.constant)

U

UCOL (in module coalispr.resources.constant) UGAPSTST (in module coalispr.resources.constant) UInt64Index (class in coalispr.resources.numeric) unbind_mousewheel() (coalispr.tk_gui.gui_widgets.opt2.Option_widget method) uncollapsed UNCOLLAPSED (in module coalispr.resources.constant) unfit_read (coalispr.bedgraph_analyze.process_bamdata.Read_checker attribute), [1] UNIQ (in module coalispr.resources.constant) unique UNMAP (in module coalispr.resources.constant) UNMAPCOLLTP (in module coalispr.resources.constant) UNMAPPEDFIL (in module coalispr.resources.constant) UNMAPTYPE (in module coalispr.resources.constant) UNSEL (in module coalispr.resources.constant) unselected UNSELFIG (in module coalispr.resources.constant) UNSPCGAPS (in module coalispr.resources.constant) unspecific

UNSPECIFIC (in module coalispr.resources.constant) unspecific() (in module coalispr.bedgraph_analyze.compare) UNSPECIFICS (in module coalispr.resources.constant) UNSPECLOG10 (in module coalispr.resources.constant) UNSPECTST (in module coalispr.resources.constant) update_args_dict() (coalispr.tk_gui.gui_widgets.opt.Options_frame method) update_multimap_count() (coalispr.bedgraph_analyze.bam_sample_counters.Bam_sample_base_controller method) (coalispr.bedgraph_analyze.bam_sample_counters.Sample_length_counter method) (coalispr.bedgraph_analyze.bam_sample_counters.Sample_region_length_counter method) update_strand_count() (coalispr.bedgraph_analyze.bam_sample_counters.Bam_sample_base_controller method) (coalispr.bedgraph_analyze.bam_sample_counters.Sample_bin_counter method) (coalispr.bedgraph_analyze.bam_sample_counters.Sample_counter method) (coalispr.bedgraph_analyze.bam_sample_counters.Sample_length_counter method) (coalispr.bedgraph_analyze.bam_sample_counters.Sample_region_length_counter method) (coalispr.bedgraph_analyze.bam_sample_counters.Sample_skip_counter method) UPPR (in module coalispr.resources.constant) USAGE (coalispr.tk_gui.gui_widgets.menu_main.Main_frame attribute) USEGAPS (in module coalispr.resources.constant)

V

VACUOL (in module coalispr.resources.constant) validate_int() (coalispr.tk_gui.gui_widgets.opt2.Option_widget method) validate_name() (coalispr.tk_gui.gui_widgets.opt2.Option_widget method)

validate_namespace() (coalispr.tk_gui.gui_widgets.opt.Options_frame method) validate_region() (coalispr.tk_gui.gui_widgets.opt2.Option_widget method) var_changed() (coalispr.tk_gui.gui_widgets.opt2.Option_widget method)

W

WCE (in module coalispr.resources.constant) widget_group (coalispr.tk_gui.gui_widgets.opt2.Subcommand_frame attribute), [1]

windows_load_font() (coalispr.tk_gui.customtkinter.font_manager.FontManager class method) WORKENV (in module coalispr.tk_gui.gui_constants) writebam (coalispr.bedgraph_analyze.process_bamdata.Bam_countprocessor attribute)

X

XGRID (in module coalispr.resources.constant) xlabel (coalispr.count_analyze.panel_plotters.PanelPlotter attribute), [1] XLIM0 (in module coalispr.resources.constant) XLIM00 (in module coalispr.resources.constant) XLIM1 (in module coalispr.resources.constant)

XLIM11 (in module coalispr.resources.constant) XLIMMAX (in module coalispr.resources.constant) XLIMMIN (in module coalispr.resources.constant) XLIMR0 (in module coalispr.resources.constant) XLIMR1 (in module coalispr.resources.constant) XTRA (in module coalispr.resources.constant)

Y

yeast (in module coalispr.resources.share.cols_from_csv_to_tab)

ylabel (coalispr.count_analyze.panel_plotters.PanelPlotter attribute), [1]

Z

ZENO (in module coalispr.tk_gui.gui_constants)

Zeros_frame_exception