Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W _ __delitem__() (panorama.systems.system.System method) __eq__() (panorama.geneFamily.GeneFamily method) (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) __getitem__() (panorama.geneFamily.Akin method) (panorama.systems.system.ClusterSystems method) (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) __hash__() (panorama.geneFamily.GeneFamily method) (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) __init__() (panorama.geneFamily.Akin method) (panorama.geneFamily.GeneFamily method) (panorama.info.info.HTMLExporter method) (panorama.info.info.PangenomeInfoExtractor method) (panorama.pangenomes.Pangenome method) (panorama.pangenomes.Pangenomes method) (panorama.region.ConservedSpots method) (panorama.region.GeneContext method) (panorama.region.Module method) (panorama.region.Region method) (panorama.region.Spot method) (panorama.systems.models._BasicFeatures method) (panorama.systems.models._FuFamFeatures method) (panorama.systems.models._ModFuFeatures method) (panorama.systems.models.Family method) (panorama.systems.models.FuncUnit method) (panorama.systems.models.Model method) (panorama.systems.models.Models method) (panorama.systems.system.ClusterSystems method) (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) (panorama.systems.systems_association.AssociationVisualizationBuilder method) (panorama.systems.systems_partitions.SystemsPartitionVisualizer method) (panorama.systems.utils.VisualizationBuilder method) __iter__() (panorama.pangenomes.Pangenomes method) (panorama.systems.models.Models method) __len__() (panorama.pangenomes.Pangenomes method) (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) __ne__() (panorama.geneFamily.GeneFamily method) __repr__() (panorama.geneFamily.GeneFamily method) (panorama.systems.models._BasicFeatures method) (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) __setitem__() (panorama.geneFamily.Akin method) (panorama.systems.system.ClusterSystems method) (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) __str__() (panorama.systems.models._BasicFeatures method) _add_families_to_functional_unit() (in module panorama.utility.translate.padloc_translator) _akin (panorama.geneFamily.GeneFamily attribute) _asso_modules() (panorama.systems.system.SystemUnit method) _BasicFeatures (class in panorama.systems.models) _calculate_max_lengths_for_system() (in module panorama.format.write_binaries) _check() (panorama.systems.models._ModFuFeatures method) _child_names() (panorama.systems.models._ModFuFeatures method) _configure_bar_plot_style() (panorama.systems.utils.VisualizationBuilder static method) _configure_minimal_plot() (panorama.systems.utils.VisualizationBuilder static method) _configure_plot_style() (panorama.systems.systems_association.AssociationVisualizationBuilder method) (panorama.systems.utils.VisualizationBuilder method) _create_boolean_filters() (panorama.info.info.HTMLExporter static method) _create_column_visibility_control() (panorama.info.info.HTMLExporter method) _create_download_button() (panorama.info.info.HTMLExporter method) _create_filter_button() (panorama.info.info.HTMLExporter method) _create_gene_family() (panorama.pangenomes.Pangenome method) _create_main_figure() (panorama.systems.utils.VisualizationBuilder method) _create_metric_plot() (panorama.systems.systems_association.AssociationVisualizationBuilder method) _create_range_sliders() (panorama.info.info.HTMLExporter method) _custom_agg() (in module panorama.systems.systems_projection) _duplicate() (panorama.systems.models._ModFuFeatures method) _execute_alignment() (in module panorama.alignment.align) _execute_cluster() (in module panorama.alignment.cluster) _execute_clustering_command() (in module panorama.alignment.cluster) _execute_linclust() (in module panorama.alignment.cluster) _extract_content() (panorama.info.info.PangenomeInfoExtractor static method) _extract_metadata() (panorama.info.info.PangenomeInfoExtractor static method) _extract_parameters() (panorama.info.info.PangenomeInfoExtractor static method) _extract_status() (panorama.info.info.PangenomeInfoExtractor static method) _families (panorama.geneFamily.Akin attribute) _FuFamFeatures (class in panorama.systems.models) _get_element_frequency() (in module panorama.systems.systems_association) _get_model_families() (panorama.systems.system.SystemUnit method) _get_region_frequency() (in module panorama.systems.systems_association) _getattr_from_ppanggolin() (panorama.geneFamily.GeneFamily method) _hmm (panorama.geneFamily.GeneFamily attribute) _layout_content_components() (panorama.info.info.HTMLExporter static method) _load_js_file() (panorama.info.info.HTMLExporter method) _make_spot_getter() (panorama.systems.system.SystemUnit method) _mk_child_getter() (panorama.systems.models._ModFuFeatures method) _mk_fam2unit() (panorama.systems.system.System method) _ModFuFeatures (class in panorama.systems.models) _prepare_mmseqs2_options() (in module panorama.alignment.cluster) _rename_content_columns() (panorama.info.info.HTMLExporter static method) _reorder_content_columns() (panorama.info.info.HTMLExporter static method) _save_figure() (panorama.systems.utils.VisualizationBuilder method) _save_html() (panorama.info.info.HTMLExporter method) _setup_slider_callbacks() (panorama.info.info.HTMLExporter method) _systems_getter (panorama.geneFamily.GeneFamily attribute) (panorama.systems.system.ClusterSystems attribute) _units_getter (panorama.geneFamily.GeneFamily attribute) _unpack_content_dict() (panorama.info.info.HTMLExporter static method) _validate_alignment_parameters() (in module panorama.alignment.align) _validate_clustering_parameters() (in module panorama.alignment.cluster) _validate_directory_access() (in module panorama.alignment.align) (in module panorama.alignment.cluster) _validate_js_files() (panorama.info.info.HTMLExporter method) _validate_seq_files() (in module panorama.alignment.utils) A accessory (panorama.systems.models._ModFuFeatures attribute) (panorama.systems.models.FuncUnit attribute) (panorama.systems.models.Model attribute) add() (panorama.geneFamily.Akin method) (panorama.pangenomes.Pangenomes method) (panorama.region.ConservedSpots method) (panorama.systems.models._ModFuFeatures method) (panorama.systems.models.FuncUnit method) (panorama.systems.models.Model method) (panorama.systems.system.ClusterSystems method) add_canonical() (panorama.systems.system.System method) add_cluster() (panorama.pangenomes.Pangenomes method) add_cluster_systems() (panorama.pangenomes.Pangenomes method) add_common_arguments() (in module panorama.utils) add_conserved_spots() (panorama.pangenomes.Pangenomes method) add_family() (panorama.systems.system.SystemUnit method) add_file() (panorama.pangenomes.Pangenome method) add_gene_family() (panorama.pangenomes.Pangenome method) add_model() (panorama.systems.models.Models method) add_module() (panorama.systems.system.SystemUnit method) add_region() (panorama.systems.system.SystemUnit method) add_spot() (panorama.pangenomes.Pangenome method) (panorama.systems.system.SystemUnit method) add_system() (panorama.pangenomes.Pangenome method) add_system_metadata_to_graph() (in module panorama.compare.systems) add_systems_info() (in module panorama.compare.spots) add_unit() (panorama.region.Module method) (panorama.systems.system.System method) Akin (class in panorama.geneFamily) akin (panorama.geneFamily.GeneFamily property) ALIGN_COLUMNS (panorama.alignment.align.AlignmentConfig attribute) align_db() (in module panorama.alignment.align) ALIGN_FORMAT (panorama.alignment.align.AlignmentConfig attribute) align_pangenomes() (in module panorama.alignment.align) align_pangenomes_pair() (in module panorama.alignment.align) AlignmentConfig (class in panorama.alignment.align) AlignmentError AlignmentValidationError all_against_all_align() (in module panorama.alignment.align) ALL_AGAINST_ALL_OUTPUT (panorama.alignment.align.AlignmentConfig attribute) annot_pangenomes() (in module panorama.annotate.annotate) annot_pangenomes_with_hmm() (in module panorama.annotate.annotate) annot_with_hmm() (in module panorama.annotate.hmm_search) annot_with_hmmscan() (in module panorama.annotate.hmm_search) annot_with_hmmsearch() (in module panorama.annotate.hmm_search) annotation_sources() (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) assign_hit() (in module panorama.annotate.hmm_search) association (panorama.systems.systems_association.AssociationVisualizationBuilder attribute) AssociationVisualizationBuilder (class in panorama.systems.systems_association) B BELOW_HEIGHT (panorama.systems.utils.VisualizationBuilder attribute) C calculate_system_table_sizes() (in module panorama.format.write_binaries) canonical (panorama.systems.models.Model attribute) (panorama.systems.system.System attribute) canonical_models() (panorama.systems.system.System method) canonical_sizes (panorama.format.write_binaries.SystemTableSizes attribute) canonical_unit_sizes (panorama.format.write_binaries.SystemTableSizes attribute) CENTER_WIDTH (panorama.systems.utils.VisualizationBuilder attribute) check_align_parameters() (in module panorama.alignment.align) check_annotate_args() (in module panorama.annotate.annotate) check_cluster_parameters() (in module panorama.alignment.cluster) check_compare_spots_args() (in module panorama.compare.spots) check_compare_systems_args() (in module panorama.compare.systems) check_context_comparison() (in module panorama.compare.context) check_detection_args() (in module panorama.systems.detection) check_dict() (in module panorama.systems.models) check_flat_parameters() (in module panorama.format.write_flat) check_for_families() (in module panorama.systems.utils) check_for_forbidden_unit() (in module panorama.systems.detection) check_for_needed_units() (in module panorama.systems.detection) check_func_unit() (panorama.systems.models.FuncUnit method) check_info_args() (in module panorama.info.info) check_input_files() (in module panorama.workflow.pansystems) check_instance_of_system() (in module panorama.systems.system) check_instance_of_system_unit() (in module panorama.systems.system) check_key() (in module panorama.systems.models) check_log() (in module panorama.utils) check_model() (panorama.systems.models.Model method) check_models() (in module panorama.utility.utility) check_needed_families() (in module panorama.systems.utils) check_pangenome_align() (in module panorama.alignment.align) check_pangenome_annotation() (in module panorama.annotate.annotate) check_pangenome_cluster() (in module panorama.alignment.cluster) check_pangenome_cs() (in module panorama.compare.spots) check_pangenome_detection() (in module panorama.systems.detection) check_pangenome_info() (in module panorama.format.read_binaries) check_pangenome_pansystems() (in module panorama.workflow.pansystems) check_pangenome_write_flat() (in module panorama.format.write_flat) check_pangenome_write_flat_annotations() (in module panorama.format.write_flat) check_pangenome_write_flat_hmm() (in module panorama.format.write_flat) check_pangenome_write_systems() (in module panorama.systems.write_systems) check_pansystems_parameters() (in module panorama.workflow.pansystems) check_parameters() (in module panorama.systems.models) (in module panorama.utility.utility) check_tsv_sanity() (in module panorama.utils) check_write_systems_args() (in module panorama.systems.write_systems) child_type (panorama.systems.models._ModFuFeatures property) CHOICES (panorama.alignment.cluster.ClusteringMethod attribute) clean_context_objects() (in module panorama.compare.context) CLUSTER (panorama.alignment.cluster.ClusteringMethod attribute) CLUSTER_COLUMN_NAMES (panorama.alignment.cluster.ClusteringConfig attribute) cluster_gene_families() (in module panorama.alignment.cluster) cluster_id (panorama.systems.system.System attribute) cluster_launcher() (in module panorama.alignment.cluster) cluster_on_gfrr() (in module panorama.compare.utils) cluster_systems (panorama.pangenomes.Pangenomes property) CLUSTERING_OUTPUT (panorama.alignment.cluster.ClusteringConfig attribute) ClusteringConfig (class in panorama.alignment.cluster) ClusteringError ClusteringMethod (class in panorama.alignment.cluster) ClusteringValidationError ClusterSystems (class in panorama.systems.system) color_bar (panorama.systems.utils.VisualizationBuilder property) common_launch() (in module panorama.compare.utils) compare_gene_contexts_graph_mp() (in module panorama.compare.context) compare_gene_contexts_on_cluster_families() (in module panorama.compare.context) compare_pair_of_context_graphs() (in module panorama.compare.context) compare_pair_of_contexts() (in module panorama.compare.context) compare_spots() (in module panorama.compare.spots) compare_systems() (in module panorama.compare.systems) compute_CCC() (in module panorama.compare.context) compute_gene_components() (in module panorama.systems.systems_projection) compute_genes_graph() (in module panorama.systems.systems_projection) compute_gfrr() (in module panorama.compare.utils) compute_gfrr_edges() (in module panorama.compare.spots) (in module panorama.compare.systems) conciliate_partition() (in module panorama.systems.utils) conserved (panorama.region.Spot property) conserved_spots (panorama.pangenomes.Pangenomes property) ConservedSpots (class in panorama.region) context_comparison() (in module panorama.compare.context) create_bar_plots() (panorama.systems.systems_association.AssociationVisualizationBuilder method) (panorama.systems.systems_partitions.SystemsPartitionVisualizer method) create_color_bar() (panorama.systems.systems_association.AssociationVisualizationBuilder method) (panorama.systems.systems_partitions.SystemsPartitionVisualizer method) create_color_palette() (panorama.systems.systems_association.AssociationVisualizationBuilder static method) create_coverage_dataframe() (in module panorama.systems.systems_association) create_coverage_plot() (panorama.systems.systems_association.AssociationVisualizationBuilder method) create_frequency_plot() (panorama.systems.systems_association.AssociationVisualizationBuilder method) create_hmm_list_file() (in module panorama.utility.genInput) create_left_bar() (panorama.systems.systems_partitions.SystemsPartitionVisualizer method) create_left_bar_plot() (panorama.systems.utils.VisualizationBuilder method) create_macsyfinder_hmm_list() (in module panorama.utility.translate.macsymodel_translator) create_main_figure() (panorama.systems.systems_association.AssociationVisualizationBuilder method) (panorama.systems.systems_partitions.SystemsPartitionVisualizer method) (panorama.systems.utils.VisualizationBuilder method) create_metanodes() (in module panorama.compare.context) create_models_list() (in module panorama.utility.utility) create_pangenome_spots_graph() (in module panorama.compare.spots) create_pangenome_system_associations() (in module panorama.systems.systems_association) create_pangenome_system_graph() (in module panorama.compare.spots) (in module panorama.compare.systems) create_pangenome_systems_heatmaps() (in module panorama.compare.systems) create_spots_graph() (in module panorama.compare.spots) create_system_description() (in module panorama.format.write_binaries) create_system_tables() (in module panorama.format.write_binaries) create_system_unit_description() (in module panorama.format.write_binaries) create_systems_graph() (in module panorama.compare.spots) (in module panorama.compare.systems) create_top_bar_plot() (panorama.systems.utils.VisualizationBuilder method) create_tsv() (in module panorama.alignment.cluster) createdb() (in module panorama.alignment.utils) custom_agg() (in module panorama.systems.systems_projection) custom_agg_unique() (in module panorama.systems.systems_projection) D DEFAULT_COV_MODE (panorama.alignment.align.AlignmentConfig attribute) (panorama.alignment.cluster.ClusteringConfig attribute) DEFAULT_COVERAGE (panorama.alignment.align.AlignmentConfig attribute) (panorama.alignment.cluster.ClusteringConfig attribute) DEFAULT_DB_TYPE (panorama.alignment.utils.MMSeqsConfig attribute) DEFAULT_EVAL (panorama.alignment.cluster.ClusteringConfig attribute) DEFAULT_FORMAT (panorama.systems.utils.VisualizationBuilder attribute) DEFAULT_IDENTITY (panorama.alignment.align.AlignmentConfig attribute) (panorama.alignment.cluster.ClusteringConfig attribute) DEFAULT_MMSEQS2_OPTIONS (panorama.alignment.cluster.ClusteringConfig attribute) DEFAULT_THREADS (panorama.alignment.align.AlignmentConfig attribute) (panorama.alignment.cluster.ClusteringConfig attribute) dict_families_context() (in module panorama.systems.utils) difference() (panorama.systems.system.SystemUnit method) digit_family_sequences() (in module panorama.annotate.hmm_search) digit_gene_sequences() (in module panorama.annotate.hmm_search) duplicate (panorama.systems.models._FuFamFeatures attribute) (panorama.systems.models.Family attribute) (panorama.systems.models.FuncUnit attribute) duplicate_fam() (panorama.systems.models.FuncUnit method) duplicate_fu() (panorama.systems.models.Model method) E eliminate_empty() (in module panorama.systems.systems_projection) eliminate_systems() (in module panorama.systems.systems_projection) erase_pangenome() (in module panorama.format.write_binaries) exchangeable (panorama.systems.models._FuFamFeatures attribute) (panorama.systems.models.Family attribute) (panorama.systems.models.FuncUnit attribute) export_content() (panorama.info.info.HTMLExporter method) export_info() (in module panorama.info.info) export_status() (panorama.info.info.HTMLExporter method) extract_info() (panorama.info.info.PangenomeInfoExtractor method) extract_numeric_for_sorting() (in module panorama.systems.systems_projection) F families (panorama.systems.models.FuncUnit property) (panorama.systems.models.Model property) (panorama.systems.models.Models property) (panorama.systems.system.System property) (panorama.systems.system.SystemUnit property) families_names() (panorama.systems.models.FuncUnit method) families_to_model() (panorama.systems.models.Models method) Family (class in panorama.systems.models) FAMILY_FILTER_ALL (panorama.alignment.utils.MMSeqsConfig attribute) filter_global_context() (in module panorama.systems.utils) filter_local_context() (in module panorama.systems.utils) filter_local_context_old() (in module panorama.systems.utils) find_cluster_canonical() (in module panorama.utility.translate.macsymodel_translator) find_type_subtype_canonical() (in module panorama.utility.translate.macsymodel_translator) forbidden (panorama.systems.models._ModFuFeatures attribute) (panorama.systems.models.FuncUnit attribute) (panorama.systems.models.Model attribute) func_unit (panorama.systems.models.Family property) func_units (panorama.systems.models.Model property) (panorama.systems.models.Models property) func_units_names() (panorama.systems.models.Model method) func_units_to_model() (panorama.systems.models.Models method) functional_unit (panorama.systems.system.SystemUnit property) FuncUnit (class in panorama.systems.models) G gene_families (panorama.pangenomes.Pangenome property) (panorama.region.Module property) GeneContext (class in panorama.region) GeneFamily (class in panorama.geneFamily) generate_heatmap() (in module panorama.compare.systems) generate_unique_accession() (in module panorama.utility.genInput) get() (panorama.geneFamily.Akin method) (panorama.pangenomes.Pangenomes method) (panorama.region.ConservedSpots method) (panorama.systems.models._ModFuFeatures method) (panorama.systems.models.FuncUnit method) (panorama.systems.models.Model method) (panorama.systems.system.ClusterSystems method) get_association_dataframes() (in module panorama.systems.systems_association) get_cluster_systems() (panorama.pangenomes.Pangenomes method) get_connected_components() (in module panorama.compare.context) get_conserved_genomics_contexts() (in module panorama.compare.context) get_conserved_spots() (panorama.pangenomes.Pangenomes method) get_contexts_from_result() (in module panorama.compare.context) get_family() (panorama.pangenomes.Pangenomes method) get_functional_unit_gene_families() (in module panorama.systems.detection) get_gene_contexts_from_results_mp() (in module panorama.compare.context) get_gene_family() (panorama.pangenomes.Pangenome method) get_gfs_matrix_combination() (in module panorama.systems.utils) get_k_best_hit() (in module panorama.annotate.annotate) get_metadata_df() (in module panorama.annotate.hmm_search) get_metadata_to_families() (in module panorama.systems.utils) get_metainfo() (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) get_model() (panorama.systems.models.Models method) get_models_path() (in module panorama.utility.translate.macsymodel_translator) get_module() (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) get_msa() (in module panorama.annotate.hmm_search) get_multigraph_edges() (in module panorama.compare.context) get_org_df() (in module panorama.systems.systems_projection) get_org_df_one_unit_per_fam() (in module panorama.systems.systems_projection) get_pangenomes_to_systems_data() (in module panorama.compare.systems) get_partition() (in module panorama.systems.systems_projection) get_region() (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) get_shortest_path_edges_cc_strategy() (in module panorama.compare.context) get_spot() (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) get_status() (in module panorama.format.read_binaries) get_subcombinations() (in module panorama.systems.detection) get_system() (panorama.pangenomes.Pangenome method) get_system_by_source() (panorama.pangenomes.Pangenome method) get_system_unit_combinations() (in module panorama.systems.detection) get_unit() (panorama.region.Module method) (panorama.systems.system.System method) glyph (panorama.systems.utils.VisualizationBuilder property) glyph_renderer (panorama.systems.utils.VisualizationBuilder property) graph_systems_link_with_conserved_spots() (in module panorama.compare.spots) H has_short_path() (in module panorama.systems.systems_projection) hash_content() (panorama.systems.system.SystemUnit method) HMM (panorama.geneFamily.GeneFamily property) HMMProcessingError HTMLExporter (class in panorama.info.info) I ID (panorama.geneFamily.Akin attribute) (panorama.systems.system.ClusterSystems attribute) (panorama.systems.system.System attribute) (panorama.systems.system.SystemUnit attribute) init_lock() (in module panorama.utils) inter_pangenome_align() (in module panorama.alignment.align) INTER_PANGENOMES_OUTPUT (panorama.alignment.align.AlignmentConfig attribute) intersection() (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) is_empty() (in module panorama.utils) is_multigenic() (panorama.geneFamily.GeneFamily method) is_multigenic_in_org() (panorama.geneFamily.GeneFamily method) is_subset() (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) is_superset() (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) is_true_value() (in module panorama.utils) items() (panorama.pangenomes.Pangenomes method) K keep_best_hit() (in module panorama.annotate.annotate) L launch() (in module panorama.alignment.align) (in module panorama.alignment.cluster) (in module panorama.annotate.annotate) (in module panorama.compare.context) (in module panorama.compare.spots) (in module panorama.compare.systems) (in module panorama.format.write_flat) (in module panorama.info.info) (in module panorama.systems.detection) (in module panorama.systems.write_systems) (in module panorama.utility.utility) (in module panorama.workflow.pansystems) launch_compare_pair_of_context_graphs() (in module panorama.compare.context) launch_context_comparison() (in module panorama.compare.context) launch_pangenomes_alignment() (in module panorama.alignment.align) launch_ppanggolin_context() (in module panorama.compare.context) launch_translate() (in module panorama.utility.translate) (in module panorama.utility.translate.translate) left_bar (panorama.systems.utils.VisualizationBuilder property) LEFT_WIDTH (panorama.systems.utils.VisualizationBuilder attribute) LINCLUST (panorama.alignment.cluster.ClusteringMethod attribute) linclust_launcher() (in module panorama.alignment.cluster) load_pangenome() (in module panorama.format.read_binaries) load_pangenomes() (in module panorama.format.read_binaries) M main_plot (panorama.systems.utils.VisualizationBuilder property) make_gene_context_from_context_graph() (in module panorama.compare.context) make_gene_context_from_context_table() (in module panorama.compare.context) mandatory (panorama.systems.models._ModFuFeatures attribute) (panorama.systems.models.FuncUnit attribute) (panorama.systems.models.Model attribute) mapper (panorama.systems.systems_partitions.SystemsPartitionVisualizer attribute) merge() (panorama.systems.system.System method) (panorama.systems.system.SystemUnit method) merge_aln_res() (in module panorama.alignment.align) MIDDLE_HEIGHT (panorama.systems.utils.VisualizationBuilder attribute) min_mandatory (panorama.systems.models._ModFuFeatures attribute) (panorama.systems.models.FuncUnit attribute) (panorama.systems.models.Model attribute) min_total (panorama.systems.models._ModFuFeatures attribute) (panorama.systems.models.FuncUnit attribute) (panorama.systems.models.Model attribute) mk_families_to_pangenome() (panorama.pangenomes.Pangenomes method) mkdir() (in module panorama.utils) MMSeqsConfig (class in panorama.alignment.utils) MMSeqsError Model (class in panorama.systems.models) model (panorama.systems.models.Family property) (panorama.systems.models.FuncUnit property) (panorama.systems.system.System attribute) (panorama.systems.system.SystemUnit property) model_families (panorama.systems.system.System property) (panorama.systems.system.SystemUnit property) model_organisms (panorama.systems.system.System property) (panorama.systems.system.SystemUnit property) Models (class in panorama.systems.models) ModelTranslationError, [1] module panorama panorama.alignment panorama.alignment.align panorama.alignment.cluster panorama.alignment.utils panorama.annotate panorama.annotate.annotate panorama.annotate.hmm_search panorama.compare panorama.compare.context panorama.compare.spots panorama.compare.systems panorama.compare.utils panorama.format panorama.format.read_binaries panorama.format.write_binaries panorama.format.write_flat panorama.format.write_proksee panorama.geneFamily panorama.info panorama.info.info panorama.main panorama.pangenomes panorama.region panorama.systems panorama.systems.detection panorama.systems.models panorama.systems.system panorama.systems.systems_association panorama.systems.systems_partitions panorama.systems.systems_projection panorama.systems.utils panorama.systems.write_systems panorama.utility panorama.utility.genInput panorama.utility.translate panorama.utility.translate.macsymodel_translator panorama.utility.translate.padloc_translator panorama.utility.translate.translate panorama.utility.utility panorama.utils panorama.workflow panorama.workflow.pansystems Module (class in panorama.region) module (panorama.geneFamily.GeneFamily property) modules (panorama.systems.system.System property) (panorama.systems.system.SystemUnit property) multi_model (panorama.systems.models._FuFamFeatures attribute) (panorama.systems.models.Family attribute) (panorama.systems.models.FuncUnit attribute) multi_system (panorama.systems.models._FuFamFeatures attribute) (panorama.systems.models.Family attribute) (panorama.systems.models.FuncUnit attribute) N name (panorama.geneFamily.GeneFamily attribute) (panorama.systems.models._BasicFeatures attribute) (panorama.systems.models.Family attribute) (panorama.systems.models.FuncUnit attribute) (panorama.systems.models.Model attribute) (panorama.systems.system.System property) (panorama.systems.system.SystemUnit property) nb_model_families (panorama.systems.system.SystemUnit property) nb_organisms (panorama.systems.system.SystemUnit property) neutral (panorama.systems.models._ModFuFeatures attribute) (panorama.systems.models.FuncUnit attribute) (panorama.systems.models.Model attribute) number_of_cluster_systems (panorama.pangenomes.Pangenomes property) number_of_conserved_spots (panorama.pangenomes.Pangenomes property) number_of_families (panorama.systems.system.System property) number_of_model_gene_families (panorama.systems.system.System property) number_of_organisms (panorama.region.Module property) (panorama.region.Spot property) number_of_systems() (panorama.pangenomes.Pangenome method) O optimized_profile (panorama.geneFamily.GeneFamily attribute) organisms (panorama.region.Module property) (panorama.region.Spot property) (panorama.systems.system.System property) (panorama.systems.system.SystemUnit property) OUTPUT_FORMATS (panorama.systems.utils.VisualizationBuilder attribute) P palette() (in module panorama.format.write_proksee) Pangenome (class in panorama.pangenomes) pangenome (panorama.systems.system.System attribute) PangenomeInfoExtractor (class in panorama.info.info) PangenomeProcessingError Pangenomes (class in panorama.pangenomes) pangenomes() (panorama.region.ConservedSpots method) (panorama.systems.system.ClusterSystems method) panorama module panorama.alignment module panorama.alignment.align module panorama.alignment.cluster module panorama.alignment.utils module panorama.annotate module panorama.annotate.annotate module panorama.annotate.hmm_search module panorama.compare module panorama.compare.context module panorama.compare.spots module panorama.compare.systems module panorama.compare.utils module panorama.format module panorama.format.read_binaries module panorama.format.write_binaries module panorama.format.write_flat module panorama.format.write_proksee module panorama.geneFamily module panorama.info module panorama.info.info module panorama.main module panorama.pangenomes module panorama.region module panorama.systems module panorama.systems.detection module panorama.systems.models module panorama.systems.system module panorama.systems.systems_association module panorama.systems.systems_partitions module panorama.systems.systems_projection module panorama.systems.utils module panorama.systems.write_systems module panorama.utility module panorama.utility.genInput module panorama.utility.translate module panorama.utility.translate.macsymodel_translator module panorama.utility.translate.padloc_translator module panorama.utility.translate.translate module panorama.utility.utility module panorama.utils module panorama.workflow module panorama.workflow.pansystems module pansystems() (in module panorama.workflow.pansystems) parse_context_results() (in module panorama.compare.context) parse_hmm_info() (in module panorama.utility.genInput) parse_macsyfinder_hmm() (in module panorama.utility.translate.macsymodel_translator) parse_meta_padloc() (in module panorama.utility.translate.padloc_translator) parser_align() (in module panorama.alignment.align) parser_annot() (in module panorama.annotate.annotate) parser_annot_hmm() (in module panorama.annotate.annotate) parser_cluster() (in module panorama.alignment.cluster) parser_comparison() (in module panorama.compare.utils) parser_comparison_context() (in module panorama.compare.context) parser_comparison_spots() (in module panorama.compare.spots) parser_comparison_systems() (in module panorama.compare.systems) parser_detection() (in module panorama.systems.detection) parser_info() (in module panorama.info.info) parser_mmseqs2_align() (in module panorama.alignment.align) parser_mmseqs2_cluster() (in module panorama.alignment.cluster) parser_pansystems() (in module panorama.workflow.pansystems) parser_utils() (in module panorama.utility.utility) parser_write() (in module panorama.format.write_flat) (in module panorama.systems.write_systems) partition2color (panorama.systems.systems_partitions.SystemsPartitionVisualizer attribute) partitions (panorama.systems.systems_partitions.SystemsPartitionVisualizer attribute) pass_graph_attribute_to_multigraph() (in module panorama.compare.context) plot() (panorama.systems.systems_association.AssociationVisualizationBuilder method) (panorama.systems.systems_partitions.SystemsPartitionVisualizer method) (panorama.systems.utils.VisualizationBuilder method) PNG_EXPORT_HEIGHT (panorama.systems.utils.VisualizationBuilder attribute) PNG_EXPORT_WIDTH (panorama.systems.utils.VisualizationBuilder attribute) pop_specific_action_grp() (in module panorama.utils) preprocess_association_data() (in module panorama.systems.systems_association) preprocess_data() (in module panorama.systems.systems_partitions) preprocess_partition_data() (in module panorama.systems.systems_partitions) presence (panorama.systems.models._FuFamFeatures attribute) (panorama.systems.models.Family attribute) (panorama.systems.models.FuncUnit attribute) process_attributes() (in module panorama.utility.translate.macsymodel_translator) process_exchangeable() (in module panorama.utility.translate.macsymodel_translator) process_hmm_accession() (in module panorama.utility.genInput) process_hmm_name() (in module panorama.utility.genInput) process_system() (in module panorama.systems.systems_association) profile (panorama.geneFamily.GeneFamily attribute) profile_gf() (in module panorama.annotate.hmm_search) profile_gfs() (in module panorama.annotate.hmm_search) project_pangenome_systems() (in module panorama.systems.systems_projection) project_unit_on_organisms() (in module panorama.systems.systems_projection) PROTEIN_FAMILIES_FILENAME (panorama.alignment.utils.MMSeqsConfig attribute) R RawTextArgumentDefaultsHelpFormatter (class in panorama.utils) read() (panorama.systems.models.Family method) (panorama.systems.models.FuncUnit method) (panorama.systems.models.Model method) (panorama.systems.models.Models method) read_clustering() (panorama.pangenomes.Pangenomes method) read_data() (in module panorama.format.write_proksee) read_families_metadata() (in module panorama.annotate.annotate) read_families_metadata_mp() (in module panorama.annotate.annotate) read_gene_families() (in module panorama.format.read_binaries) read_gene_families_info() (in module panorama.format.read_binaries) read_hmm() (in module panorama.utility.genInput) read_hmms() (in module panorama.annotate.hmm_search) read_metadata() (in module panorama.utility.genInput) read_model() (panorama.systems.models.Model static method) read_modules() (in module panorama.format.read_binaries) read_pangenome() (in module panorama.format.read_binaries) read_parameters() (panorama.systems.models._BasicFeatures method) read_settings() (in module panorama.format.write_proksee) read_spots() (in module panorama.format.read_binaries) read_systems() (in module panorama.format.read_binaries) read_systems_by_source() (in module panorama.format.read_binaries) read_xml() (in module panorama.utility.translate) (in module panorama.utility.translate.translate) read_yaml() (in module panorama.utility.translate) (in module panorama.utility.translate.translate) recast() (panorama.geneFamily.GeneFamily static method) reference (panorama.geneFamily.Akin attribute) Region (class in panorama.region) regions (panorama.systems.system.System property) (panorama.systems.system.SystemUnit property) remove_redundant_annotation() (in module panorama.annotate.annotate) RIGHT_WIDTH (panorama.systems.utils.VisualizationBuilder attribute) S same_strand (panorama.systems.models._ModFuFeatures attribute) (panorama.systems.models.FuncUnit attribute) (panorama.systems.models.Model attribute) search_canonical_macsyfinder() (in module panorama.utility.translate.macsymodel_translator) search_canonical_padloc() (in module panorama.utility.translate.padloc_translator) search_for_system() (in module panorama.systems.detection) search_system() (in module panorama.systems.detection) search_system_units() (in module panorama.systems.detection) search_systems() (in module panorama.systems.detection) search_systems_in_pangenomes() (in module panorama.systems.detection) search_unit_in_cc() (in module panorama.systems.detection) search_unit_in_combination() (in module panorama.systems.detection) search_unit_in_context() (in module panorama.systems.detection) set_verbosity_level() (in module panorama.utils) size (panorama.systems.models.FuncUnit property) (panorama.systems.models.Model property) (panorama.systems.models.Models property) source (panorama.systems.system.System attribute) (panorama.systems.system.SystemUnit attribute) Spot (class in panorama.region) spots (panorama.region.ConservedSpots property) (panorama.systems.system.System property) (panorama.systems.system.SystemUnit property) subparser() (in module panorama.alignment.align) (in module panorama.alignment.cluster) (in module panorama.annotate.annotate) (in module panorama.compare.context) (in module panorama.compare.spots) (in module panorama.compare.systems) (in module panorama.format.write_flat) (in module panorama.info.info) (in module panorama.systems.detection) (in module panorama.systems.write_systems) (in module panorama.utility.utility) (in module panorama.workflow.pansystems) summarize() (panorama.region.GeneContext method) symmetric_difference() (panorama.systems.system.SystemUnit method) System (class in panorama.systems.system) system (panorama.systems.system.SystemUnit property) system_projection() (in module panorama.systems.systems_projection) system_sizes (panorama.format.write_binaries.SystemTableSizes attribute) system_to_canonical_rows (panorama.format.write_binaries.SystemTableSizes attribute) systems (panorama.pangenomes.Pangenome property) (panorama.region.Module property) (panorama.systems.system.ClusterSystems property) systems_partition() (in module panorama.systems.systems_partitions) systems_sources (panorama.pangenomes.Pangenome property) systems_sources_to_metadata_source() (panorama.pangenomes.Pangenome method) SystemsComparisonError SystemsPartitionVisualizer (class in panorama.systems.systems_partitions) SystemTableSizes (class in panorama.format.write_binaries) SystemUnit (class in panorama.systems.system) T to_list() (panorama.pangenomes.Pangenomes method) to_set() (panorama.pangenomes.Pangenomes method) top_bar (panorama.systems.utils.VisualizationBuilder property) TOP_HEIGHT (panorama.systems.utils.VisualizationBuilder attribute) TOTAL_HEIGHT (panorama.systems.utils.VisualizationBuilder attribute) TOTAL_WIDTH (panorama.systems.utils.VisualizationBuilder attribute) transitivity (panorama.systems.models._BasicFeatures attribute) (panorama.systems.models.Family attribute) (panorama.systems.models.FuncUnit attribute) (panorama.systems.models.Model attribute) translate_functional_unit() (in module panorama.utility.translate.macsymodel_translator) translate_gene() (in module panorama.utility.translate.macsymodel_translator) translate_macsyfinder() (in module panorama.utility.translate.macsymodel_translator) translate_macsyfinder_model() (in module panorama.utility.translate.macsymodel_translator) translate_model_padloc() (in module panorama.utility.translate.padloc_translator) translate_padloc() (in module panorama.utility.translate.padloc_translator) U unit_projection() (in module panorama.systems.systems_projection) unit_sizes (panorama.format.write_binaries.SystemTableSizes attribute) units (panorama.region.Module property) (panorama.systems.system.System property) V value (panorama.systems.models.Models property) VisualizationBuilder (class in panorama.systems.utils) W window (panorama.systems.models._BasicFeatures attribute) (panorama.systems.models.Family attribute) (panorama.systems.models.FuncUnit attribute) (panorama.systems.models.Model attribute) write_alignment() (in module panorama.alignment.align) write_annotations_to_pangenome() (in module panorama.annotate.annotate) write_annotations_to_pangenomes() (in module panorama.annotate.annotate) write_clustering() (in module panorama.alignment.cluster) write_conserved_spots() (in module panorama.compare.spots) write_conserved_systems() (in module panorama.compare.systems) write_context_summary() (in module panorama.compare.context) write_contig() (in module panorama.format.write_proksee) write_correlation_matrix_visualization() (in module panorama.systems.systems_association) write_flat_files() (in module panorama.format.write_flat) write_flat_systems_to_pangenome() (in module panorama.systems.write_systems) write_genes() (in module panorama.format.write_proksee) write_hmm() (in module panorama.format.write_flat) (in module panorama.utility.genInput) write_hmm_profile() (in module panorama.format.write_flat) write_legend_items() (in module panorama.format.write_proksee) write_model() (in module panorama.utility.translate.translate) write_modules() (in module panorama.format.write_proksee) write_pangenome() (in module panorama.format.write_binaries) write_pangenome_families_annotations() (in module panorama.format.write_flat) write_pangenome_status() (in module panorama.format.write_binaries) write_pangenomes_families_annotations() (in module panorama.format.write_flat) write_pangenomes_families_sequences() (in module panorama.alignment.utils) write_pangenomes_systems() (in module panorama.systems.write_systems) write_partition() (in module panorama.format.write_proksee) write_projection_systems() (in module panorama.systems.systems_projection) write_proksee() (in module panorama.format.write_proksee) write_proksee_organism() (in module panorama.format.write_proksee) write_protein_families_sequences() (in module panorama.alignment.utils) write_rgp() (in module panorama.format.write_proksee) write_spots() (in module panorama.format.write_proksee) write_system_data_to_tables() (in module panorama.format.write_binaries) write_systems() (in module panorama.format.write_proksee) write_systems_to_hdf5() (in module panorama.format.write_binaries) write_systems_to_pangenome() (in module panorama.systems.detection) write_systems_to_pangenomes() (in module panorama.systems.detection) write_top_hits() (in module panorama.annotate.hmm_search) write_tracks() (in module panorama.format.write_proksee)
