Index

A

add() (ppanggolin.geneFamily.GeneFamily method) (ppanggolin.genome.Contig method) (ppanggolin.genome.Organism method) (ppanggolin.region.Module method) (ppanggolin.region.Region method) (ppanggolin.region.Spot method) add_common_arguments() (in module ppanggolin.utils) add_contig_length() (ppanggolin.genome.Contig method) add_edge() (ppanggolin.pangenome.Pangenome method) add_edges_to_context_graph() (in module ppanggolin.context.searchGeneContext) add_edges_to_identical_rgps() (in module ppanggolin.RGP.rgp_cluster) add_family() (ppanggolin.region.GeneContext method) add_file() (ppanggolin.pangenome.Pangenome method) add_gene() (in module ppanggolin.utils) add_gene_family() (ppanggolin.pangenome.Pangenome method) add_gene_labels() (in module ppanggolin.figures.draw_spot) add_gene_tools() (in module ppanggolin.figures.draw_spot) add_genes() (ppanggolin.edge.Edge method) add_genome_tools() (in module ppanggolin.figures.draw_spot) add_info_to_identical_rgps() (in module ppanggolin.RGP.rgp_cluster) add_info_to_rgp_nodes() (in module ppanggolin.RGP.rgp_cluster) add_metadata() (ppanggolin.metadata.MetaFeatures method)

add_metadata_from_gff_file() (in module ppanggolin.annotate.annotate) add_module() (ppanggolin.pangenome.Pangenome method) add_new_node_in_spot_graph() (in module ppanggolin.RGP.spot) add_organism() (ppanggolin.pangenome.Pangenome method) add_protein() (ppanggolin.genome.Gene method) add_region() (ppanggolin.pangenome.Pangenome method) add_rgp_metadata_to_graph() (in module ppanggolin.RGP.rgp_cluster) add_rna() (ppanggolin.genome.Contig method) add_sequence() (ppanggolin.geneFamily.GeneFamily method) (ppanggolin.genome.Feature method) add_spot() (ppanggolin.geneFamily.GeneFamily method) (ppanggolin.pangenome.Pangenome method) add_val_to_dict_attribute() (in module ppanggolin.context.searchGeneContext) add_workflow_args() (in module ppanggolin.workflow.all) align() (in module ppanggolin.align.alignOnPang) align_rep() (in module ppanggolin.cluster.cluster) align_seq_to_pang() (in module ppanggolin.align.alignOnPang) align_sequences_to_families() (in module ppanggolin.context.searchGeneContext) annotate_fasta_files() (in module ppanggolin.projection.projection) annotate_input_genes_with_pangenome_families() (in module ppanggolin.projection.projection) annotate_organism() (in module ppanggolin.annotate.synta) annotate_pangenome() (in module ppanggolin.annotate.annotate) assign_metadata() (in module ppanggolin.meta.meta)

B

borders() (ppanggolin.region.Spot method)

build_presence_absence_matrix() (in module ppanggolin.figures.tile_plot) build_ucurve_plot() (in module ppanggolin.figures.ucurve)

C

changes() (ppanggolin.RGP.genomicIsland.MatriceNode method) check_already_computed_metric() (in module ppanggolin.metrics.metrics) check_and_add_extra_gene_part() (in module ppanggolin.annotate.annotate) check_annotate_args() (in module ppanggolin.annotate.annotate) check_config_consistency() (in module ppanggolin.utils) check_input_files() (in module ppanggolin.utils) check_input_names() (in module ppanggolin.projection.projection) check_log() (in module ppanggolin.utils) check_metadata_arguments() (in module ppanggolin.meta.meta) check_metadata_format() (in module ppanggolin.meta.meta) check_option_workflow() (in module ppanggolin.utils) check_pangenome_for_clustering() (in module ppanggolin.cluster.cluster) check_pangenome_for_context_search() (in module ppanggolin.context.searchGeneContext) check_pangenome_for_neighbors_graph() (in module ppanggolin.graph.makeGraph) check_pangenome_for_projection() (in module ppanggolin.projection.projection) check_pangenome_former_clustering() (in module ppanggolin.cluster.cluster) check_pangenome_former_graph() (in module ppanggolin.graph.makeGraph) check_pangenome_former_modules() (in module ppanggolin.mod.module) check_pangenome_former_partition() (in module ppanggolin.nem.partition) check_pangenome_former_rgp() (in module ppanggolin.RGP.genomicIsland) check_pangenome_former_spots() (in module ppanggolin.RGP.spot) check_pangenome_info() (in module ppanggolin.formats.readBinaries) check_pangenome_metadata() (in module ppanggolin.meta.meta) check_predicted_spots() (in module ppanggolin.figures.draw_spot) check_projection_arguments() (in module ppanggolin.projection.projection) check_sequence_tuple() (in module ppanggolin.annotate.synta) check_sim() (in module ppanggolin.RGP.spot) check_spot_args() (in module ppanggolin.figures.drawing) check_spots_congruency() (in module ppanggolin.projection.projection) check_tools_availability() (in module ppanggolin.utils) check_translation_table() (in module ppanggolin.workflow.all) check_translation_table_to_use() (in module ppanggolin.utils) check_tsv_sanity() (in module ppanggolin.utils) check_version_compatibility() (in module ppanggolin.utils) check_write_sequences_args() (in module ppanggolin.formats.writeSequences) chose_gene_identifiers() (in module ppanggolin.annotate.annotate) cluster_rgp() (in module ppanggolin.RGP.rgp_cluster) cluster_rgp_on_grr() (in module ppanggolin.RGP.rgp_cluster) clustering() (in module ppanggolin.cluster.cluster) cmd_line() (in module ppanggolin.main)

combine_args() (in module ppanggolin.utils) combine_contigs_metadata() (in module ppanggolin.annotate.annotate) comp_border() (in module ppanggolin.RGP.spot) compute_edge_metrics() (in module ppanggolin.context.searchGeneContext) compute_family_bitarrays() (ppanggolin.pangenome.Pangenome method) compute_family_counts() (in module ppanggolin.figures.ucurve) compute_gene_context_graph() (in module ppanggolin.context.searchGeneContext) compute_genomes_fluidity() (in module ppanggolin.metrics.fluidity) compute_grr() (in module ppanggolin.RGP.rgp_cluster) compute_jaccard_index() (in module ppanggolin.RGP.rgp_cluster) compute_metrics() (in module ppanggolin.metrics.metrics) compute_mod_bitarrays() (ppanggolin.pangenome.Pangenome method) compute_mod_graph() (in module ppanggolin.mod.module) compute_modules() (in module ppanggolin.mod.module) compute_msa() (in module ppanggolin.formats.writeMSA) compute_neighbors_graph() (in module ppanggolin.graph.makeGraph) compute_org_bitarrays() (ppanggolin.pangenome.Pangenome method) compute_org_rgp() (in module ppanggolin.RGP.genomicIsland) compute_rgp_metric() (in module ppanggolin.RGP.rgp_cluster) connected_components() (in module ppanggolin.utils) contains_gene_id() (ppanggolin.geneFamily.GeneFamily method) Contig (class in ppanggolin.genome) contig (ppanggolin.genome.Feature property) (ppanggolin.region.Region property) contig_desc() (in module ppanggolin.formats.writeAnnotations) contig_lengths_unavailable() (ppanggolin.pangenome.Pangenome method) contigs (ppanggolin.genome.Organism property) (ppanggolin.pangenome.Pangenome property) convert_overlapping_coordinates_for_gff() (in module ppanggolin.formats.writeFlatGenomes) coordinates (ppanggolin.region.Region property) correct_putative_overlaps() (in module ppanggolin.annotate.annotate) count_neighbors_partitions() (in module ppanggolin.formats.writeFlatGenomes) count_uniq_content() (ppanggolin.region.Spot method) count_uniq_ordered_set() (ppanggolin.region.Spot method) create_gene() (in module ppanggolin.annotate.annotate) create_info_dict() (in module ppanggolin.formats.readBinaries) create_mmseqs_db() (in module ppanggolin.formats.writeSequences) create_partition_shapes() (in module ppanggolin.figures.tile_plot) create_tile_plot() (in module ppanggolin.figures.tile_plot) create_tmpdir() (in module ppanggolin.utils)

D

deduplicate_actions() (in module ppanggolin.utility.utils) del_metadata_by_attribute() (ppanggolin.metadata.MetaFeatures method) del_metadata_by_source() (ppanggolin.metadata.MetaFeatures method) delete_unspecified_args() (in module ppanggolin.utils) dereplicate_rgp() (in module ppanggolin.RGP.rgp_cluster) desc_metadata() (in module ppanggolin.formats.writeMetadata) detect_filetype() (in module ppanggolin.utils) determine_genetic_code_from_annotation_files() (in module ppanggolin.annotate.annotate)

determine_genetic_code_to_use() (in module ppanggolin.annotate.annotate) draw_curr_spot() (in module ppanggolin.figures.draw_spot) draw_curve() (in module ppanggolin.nem.rarefaction) draw_selected_spots() (in module ppanggolin.figures.draw_spot) draw_spot_gexf() (in module ppanggolin.align.alignOnPang) draw_spots() (in module ppanggolin.figures.draw_spot) draw_tile_plot() (in module ppanggolin.figures.tile_plot) draw_ucurve() (in module ppanggolin.figures.ucurve) duplication_ratio() (ppanggolin.geneFamily.GeneFamily method)

E

Edge (class in ppanggolin.edge) edges (ppanggolin.geneFamily.GeneFamily property) (ppanggolin.pangenome.Pangenome property) encode_attribute_val() (in module ppanggolin.formats.writeFlatGenomes) encode_attributes() (in module ppanggolin.formats.writeFlatGenomes) erase_default_value() (in module ppanggolin.utils) erase_metadata() (in module ppanggolin.formats.writeMetadata)

erase_pangenome() (in module ppanggolin.formats.writeBinaries) evaluate_nb_partitions() (in module ppanggolin.nem.partition) exact_core_families() (ppanggolin.pangenome.Pangenome method) export_context_to_dataframe() (in module ppanggolin.context.searchGeneContext) extract_contig_window() (in module ppanggolin.utils) extract_positions() (in module ppanggolin.annotate.annotate) extract_rgp() (in module ppanggolin.RGP.genomicIsland)

F

fam_fluidity() (in module ppanggolin.metrics.fluidity) fam_to_seq() (in module ppanggolin.context.searchGeneContext) families (ppanggolin.genome.Contig property) (ppanggolin.genome.Organism property) (ppanggolin.region.GeneContext property) (ppanggolin.region.Module property) (ppanggolin.region.Region property) (ppanggolin.region.Spot property) family (ppanggolin.genome.Gene property) Feature (class in ppanggolin.genome) fields (ppanggolin.metadata.Metadata property) fill_annotations() (ppanggolin.genome.Feature method) (ppanggolin.genome.Gene method)

fill_parents() (ppanggolin.genome.Feature method) filter_values() (in module ppanggolin.formats.writeSequences) find_consecutive_sequences() (in module ppanggolin.utils) find_region_border_position() (in module ppanggolin.utils) first_clustering() (in module ppanggolin.cluster.cluster) fix_partial_gene_coordinates() (in module ppanggolin.annotate.annotate) flatten_nested_dict() (in module ppanggolin.utils) format_rgp_metadata() (in module ppanggolin.RGP.rgp_cluster) formatted_metadata_dict() (ppanggolin.metadata.MetaFeatures method) formatted_metadata_dict_to_string() (ppanggolin.metadata.MetaFeatures method) frame (ppanggolin.genome.Gene property)

G

Gene (class in ppanggolin.genome) gene_desc() (in module ppanggolin.formats.writeAnnotations) gene_fam_desc() (in module ppanggolin.formats.writeBinaries) gene_families (ppanggolin.pangenome.Pangenome property) gene_joined_coordinates_desc() (in module ppanggolin.formats.writeAnnotations) gene_pairs (ppanggolin.edge.Edge property) gene_sequences_desc() (in module ppanggolin.formats.writeAnnotations) gene_to_fam_desc() (in module ppanggolin.formats.writeBinaries) GeneContext (class in ppanggolin.region) Genedata (class in ppanggolin.formats.readBinaries) genedata_desc() (in module ppanggolin.formats.writeAnnotations) GeneFamily (class in ppanggolin.geneFamily) generate_dendrogram() (in module ppanggolin.figures.tile_plot) genes (ppanggolin.geneFamily.GeneFamily property) (ppanggolin.genome.Contig property) (ppanggolin.genome.Organism property) (ppanggolin.pangenome.Pangenome property) (ppanggolin.region.Region property) (ppanggolin.RGP.rgp_cluster.IdenticalRegions property) genetic_codes() (in module ppanggolin.genetic_codes) get() (ppanggolin.geneFamily.GeneFamily method) (ppanggolin.genome.Organism method) (ppanggolin.region.Module method) (ppanggolin.region.Region method) (ppanggolin.region.Spot method) get_arg_name() (in module ppanggolin.utils) get_arg_names_from_namespace() (in module ppanggolin.utils) get_args_differing_from_default() (in module ppanggolin.utils) get_bordering_genes() (ppanggolin.region.Region method) get_by_coordinate() (ppanggolin.genome.Contig method) get_cli_args() (in module ppanggolin.utils) get_config_args() (in module ppanggolin.utils) get_consecutive_region_positions() (in module ppanggolin.utils) get_contig() (ppanggolin.pangenome.Pangenome method) get_contig_to_genes() (in module ppanggolin.context.searchGeneContext) get_contigs_from_fasta_file() (in module ppanggolin.annotate.synta) get_default_args() (in module ppanggolin.utils) get_default_argument_lines() (in module ppanggolin.utility.utils) get_dna_sequence() (in module ppanggolin.annotate.synta) get_edge() (ppanggolin.geneFamily.GeneFamily method) get_elem_by_metadata() (ppanggolin.pangenome.Pangenome method) get_elem_by_source() (ppanggolin.pangenome.Pangenome method) get_fam_index() (ppanggolin.pangenome.Pangenome method) get_fam_to_rgp() (in module ppanggolin.align.alignOnPang) get_fam_to_spot() (in module ppanggolin.align.alignOnPang) get_families_from_genes() (in module ppanggolin.formats.readBinaries) get_families_matching_partition() (in module ppanggolin.formats.readBinaries) get_families_to_write() (in module ppanggolin.formats.writeMSA) get_family_representative_sequences() (in module ppanggolin.cluster.cluster) get_family_to_genome_count() (in module ppanggolin.formats.readBinaries) get_gene() (ppanggolin.pangenome.Pangenome method) get_gene_contexts() (in module ppanggolin.context.searchGeneContext) get_gene_fam_len() (in module ppanggolin.formats.writeBinaries) get_gene_family() (ppanggolin.pangenome.Pangenome method) get_gene_id_len() (in module ppanggolin.formats.writeBinaries) get_gene_sequences_from_fasta_files() (in module ppanggolin.projection.projection) get_gene_sequences_from_fastas() (in module ppanggolin.annotate.annotate)

get_gene_sequences_len() (in module ppanggolin.formats.writeAnnotations) get_gene_to_fam_len() (in module ppanggolin.formats.writeBinaries) get_gene_to_genome() (in module ppanggolin.formats.readBinaries) get_genedata() (in module ppanggolin.formats.writeAnnotations) get_genes() (ppanggolin.genome.Contig method) get_genes_from_families() (in module ppanggolin.formats.readBinaries) get_genes_per_org() (ppanggolin.geneFamily.GeneFamily method) get_heatmap_hover_text() (in module ppanggolin.figures.tile_plot) get_input_argument_lines() (in module ppanggolin.utility.utils) get_input_seq_to_family_with_all() (in module ppanggolin.align.alignOnPang) get_input_seq_to_family_with_rep() (in module ppanggolin.align.alignOnPang) get_major_version() (in module ppanggolin.utils) get_max_len_annotations() (in module ppanggolin.formats.writeAnnotations) get_max_len_genedata() (in module ppanggolin.formats.writeAnnotations) get_metadata() (ppanggolin.metadata.MetaFeatures method) get_metadata_by_attribute() (ppanggolin.metadata.MetaFeatures method) get_metadata_by_source() (ppanggolin.metadata.MetaFeatures method) get_metadata_contig_len() (in module ppanggolin.formats.writeMetadata) get_metadata_len() (in module ppanggolin.formats.writeMetadata) get_mod_desc() (in module ppanggolin.formats.writeBinaries) get_module() (ppanggolin.pangenome.Pangenome method) get_multigenics() (ppanggolin.pangenome.Pangenome method) get_n_next_genes_index() (in module ppanggolin.context.searchGeneContext) get_need_info() (in module ppanggolin.formats.readBinaries) get_non_redundant_gene_sequences_from_file() (in module ppanggolin.formats.readBinaries) get_number_of_organisms() (in module ppanggolin.formats.readBinaries) get_ordered_consecutive_genes() (ppanggolin.genome.Contig method) get_ordered_genes() (ppanggolin.region.Region method) get_org_dict() (ppanggolin.geneFamily.GeneFamily method) get_org_index() (ppanggolin.pangenome.Pangenome method) get_organism() (ppanggolin.pangenome.Pangenome method) get_organism_genes_pairs() (ppanggolin.edge.Edge method) get_organism_list() (in module ppanggolin.formats.writeFlatGenomes) get_organisms_dict() (ppanggolin.edge.Edge method) get_pangenome_parameters() (in module ppanggolin.formats.readBinaries) get_region() (ppanggolin.pangenome.Pangenome method) get_rgp_len() (in module ppanggolin.formats.writeBinaries) get_seq_ids() (in module ppanggolin.align.alignOnPang) get_seq_info() (in module ppanggolin.align.alignOnPang) get_seqid_to_genes() (in module ppanggolin.formats.readBinaries) get_sequence_len() (in module ppanggolin.formats.writeAnnotations) get_single_copy_persistent_families() (ppanggolin.pangenome.Pangenome method) get_soft_core_families() (in module ppanggolin.formats.readBinaries) get_spot() (ppanggolin.pangenome.Pangenome method) get_spot_desc() (in module ppanggolin.formats.writeBinaries) get_spot_id() (in module ppanggolin.RGP.rgp_cluster) get_status() (in module ppanggolin.formats.readBinaries) get_subcommand_parser() (in module ppanggolin.utils) get_uniq_content() (ppanggolin.region.Spot method) get_uniq_ordered_set() (ppanggolin.region.Spot method) get_uniq_to_rgp() (ppanggolin.region.Spot method) getmax() (in module ppanggolin.formats.writeBinaries) getmean() (in module ppanggolin.formats.writeBinaries) getmin() (in module ppanggolin.formats.writeBinaries) getstdev() (in module ppanggolin.formats.writeBinaries) graph (ppanggolin.region.GeneContext property) graph_desc() (in module ppanggolin.formats.writeBinaries) group_genes_by_partition() (ppanggolin.genome.Organism method)

H

has_joined_coordinates (ppanggolin.genome.Feature property) has_metadata() (ppanggolin.metadata.MetaFeatures method) (ppanggolin.pangenome.Pangenome method)

has_module (ppanggolin.geneFamily.GeneFamily property) has_non_ascii() (in module ppanggolin.utils) has_source() (ppanggolin.metadata.MetaFeatures method)

I

id_counter (ppanggolin.region.Region attribute) IdenticalRegions (class in ppanggolin.RGP.rgp_cluster) identify_rgp_last_and_first_genes() (ppanggolin.region.Region method) increment_attribute_counter() (in module ppanggolin.context.searchGeneContext) infer_input_mode() (in module ppanggolin.projection.projection) infer_singletons() (in module ppanggolin.cluster.cluster) init_contig_counter() (in module ppanggolin.annotate.synta)

init_matrices() (in module ppanggolin.RGP.genomicIsland) initiate_proksee_data() (in module ppanggolin.formats.write_proksee) is_compressed() (in module ppanggolin.utils) is_contig_border (ppanggolin.region.Region property) is_gene_list_ordered() (in module ppanggolin.figures.draw_spot) is_single_copy() (ppanggolin.geneFamily.GeneFamily method) is_whole_contig (ppanggolin.region.Region property)

J

jaccard_similarities() (in module ppanggolin.utils)

join_dicts() (in module ppanggolin.RGP.rgp_cluster)

L

launch() (in module ppanggolin.align.alignOnPang) (in module ppanggolin.annotate.annotate) (in module ppanggolin.cluster.cluster) (in module ppanggolin.context.searchGeneContext) (in module ppanggolin.figures.drawing) (in module ppanggolin.formats.writeFlatGenomes) (in module ppanggolin.formats.writeFlatPangenome) (in module ppanggolin.formats.writeMSA) (in module ppanggolin.formats.writeSequences) (in module ppanggolin.graph.makeGraph) (in module ppanggolin.info.info) (in module ppanggolin.meta.meta) (in module ppanggolin.metrics.metrics) (in module ppanggolin.mod.module) (in module ppanggolin.nem.partition) (in module ppanggolin.nem.rarefaction) (in module ppanggolin.projection.projection) (in module ppanggolin.RGP.genomicIsland) (in module ppanggolin.RGP.rgp_cluster) (in module ppanggolin.RGP.spot) (in module ppanggolin.utility.utils) (in module ppanggolin.workflow.all) (in module ppanggolin.workflow.panModule) (in module ppanggolin.workflow.panRGP) (in module ppanggolin.workflow.workflow)

launch_aragorn() (in module ppanggolin.annotate.synta) launch_default_config() (in module ppanggolin.utility.utils) launch_infernal() (in module ppanggolin.annotate.synta) launch_mafft() (in module ppanggolin.formats.writeMSA) launch_multi_mafft() (in module ppanggolin.formats.writeMSA) launch_prodigal() (in module ppanggolin.annotate.synta) launch_raref_nem() (in module ppanggolin.nem.rarefaction) launch_workflow() (in module ppanggolin.workflow.all) length (ppanggolin.genome.Contig property) (ppanggolin.region.Region property) line_order_gene_lists() (in module ppanggolin.figures.draw_spot) local_identifiers_are_unique() (in module ppanggolin.annotate.annotate)

M

main() (in module ppanggolin.main) make_colors_for_iterable() (in module ppanggolin.figures.draw_spot) make_graph_writable() (in module ppanggolin.context.searchGeneContext) make_rarefaction_curve() (in module ppanggolin.nem.rarefaction) make_spot_graph() (in module ppanggolin.RGP.spot) manage_annotate_param() (in module ppanggolin.projection.projection) manage_cli_and_config_args() (in module ppanggolin.utils) manage_input_genomes_annotation() (in module ppanggolin.projection.projection) manage_module_colors() (in module ppanggolin.formats.writeFlatGenomes) map_input_gene_to_family_all_aln() (in module ppanggolin.align.alignOnPang) map_input_gene_to_family_rep_aln() (in module ppanggolin.align.alignOnPang) MatriceNode (class in ppanggolin.RGP.genomicIsland) max_fam_id (ppanggolin.pangenome.Pangenome property) max_metadata_by_source() (ppanggolin.metadata.MetaFeatures method) Metadata (class in ppanggolin.metadata) metadata (ppanggolin.metadata.MetaFeatures property) metadata() (ppanggolin.pangenome.Pangenome method) metadata_sources() (ppanggolin.pangenome.Pangenome method) metadata_stringify() (in module ppanggolin.figures.tile_plot) MetaFeatures (class in ppanggolin.metadata) min_one() (in module ppanggolin.utils) mk_bitarray() (ppanggolin.geneFamily.GeneFamily method) (ppanggolin.genome.Organism method) (ppanggolin.region.Module method) mk_file_name() (in module ppanggolin.utils) mk_genomes() (in module ppanggolin.figures.draw_spot) mk_local_to_gene() (in module ppanggolin.cluster.cluster) mk_outdir() (in module ppanggolin.utils) mk_regions() (in module ppanggolin.RGP.genomicIsland) mk_source_data() (in module ppanggolin.figures.draw_spot) mod_desc() (in module ppanggolin.formats.writeBinaries) module ppanggolin ppanggolin.align ppanggolin.align.alignOnPang ppanggolin.annotate ppanggolin.annotate.annotate ppanggolin.annotate.synta ppanggolin.cluster ppanggolin.cluster.cluster ppanggolin.context ppanggolin.context.searchGeneContext ppanggolin.edge ppanggolin.figures ppanggolin.figures.draw_spot ppanggolin.figures.drawing ppanggolin.figures.tile_plot ppanggolin.figures.ucurve ppanggolin.formats ppanggolin.formats.readBinaries ppanggolin.formats.write_proksee ppanggolin.formats.writeAnnotations ppanggolin.formats.writeBinaries ppanggolin.formats.writeFlatGenomes ppanggolin.formats.writeFlatPangenome ppanggolin.formats.writeMetadata ppanggolin.formats.writeMSA ppanggolin.formats.writeSequences ppanggolin.geneFamily ppanggolin.genetic_codes ppanggolin.genome ppanggolin.graph ppanggolin.graph.makeGraph ppanggolin.info ppanggolin.info.info ppanggolin.main ppanggolin.meta ppanggolin.meta.meta ppanggolin.metadata ppanggolin.metrics ppanggolin.metrics.fluidity ppanggolin.metrics.metrics ppanggolin.mod ppanggolin.mod.module ppanggolin.nem ppanggolin.nem.partition ppanggolin.nem.rarefaction ppanggolin.pangenome ppanggolin.projection ppanggolin.projection.projection ppanggolin.region ppanggolin.RGP ppanggolin.RGP.genomicIsland ppanggolin.RGP.rgp_cluster ppanggolin.RGP.spot ppanggolin.utility ppanggolin.utility.utils ppanggolin.utils ppanggolin.workflow ppanggolin.workflow.all ppanggolin.workflow.panModule ppanggolin.workflow.panRGP ppanggolin.workflow.workflow

Module (class in ppanggolin.region) module (ppanggolin.geneFamily.GeneFamily property) (ppanggolin.genome.Gene property) modules (ppanggolin.genome.Contig property) (ppanggolin.genome.Organism property) (ppanggolin.pangenome.Pangenome property) (ppanggolin.region.Region property) (ppanggolin.RGP.rgp_cluster.IdenticalRegions property) mp_write_genomes_file() (in module ppanggolin.formats.writeFlatGenomes)

N

named_partition (ppanggolin.geneFamily.GeneFamily property) naming_scheme() (in module ppanggolin.RGP.genomicIsland) nb_fam_per_org() (in module ppanggolin.metrics.fluidity) nb_org_per_fam() (in module ppanggolin.metrics.fluidity) neighbors (ppanggolin.geneFamily.GeneFamily property) nem_samples() (in module ppanggolin.nem.partition) nem_single() (in module ppanggolin.nem.partition) NewSpot (class in ppanggolin.projection.projection) number_of_contigs (ppanggolin.genome.Organism property) (ppanggolin.pangenome.Pangenome property) number_of_edges (ppanggolin.geneFamily.GeneFamily property) (ppanggolin.pangenome.Pangenome property) number_of_families (ppanggolin.region.Region property) (ppanggolin.region.Spot property) number_of_families() (ppanggolin.genome.Organism method) number_of_gene_families (ppanggolin.pangenome.Pangenome property) number_of_genes (ppanggolin.geneFamily.GeneFamily property) (ppanggolin.genome.Contig property) (ppanggolin.pangenome.Pangenome property)

number_of_genes() (ppanggolin.genome.Organism method) number_of_metadata (ppanggolin.metadata.MetaFeatures property) number_of_modules (ppanggolin.genome.Organism property) (ppanggolin.pangenome.Pangenome property) number_of_neighbors (ppanggolin.geneFamily.GeneFamily property) number_of_organisms (ppanggolin.edge.Edge property) (ppanggolin.geneFamily.GeneFamily property) (ppanggolin.pangenome.Pangenome property) number_of_regions (ppanggolin.genome.Organism property) number_of_rgp (ppanggolin.pangenome.Pangenome property) number_of_rnas (ppanggolin.genome.Contig property) (ppanggolin.pangenome.Pangenome property) number_of_rnas() (ppanggolin.genome.Organism method) number_of_spots (ppanggolin.geneFamily.GeneFamily property) (ppanggolin.genome.Organism property) (ppanggolin.pangenome.Pangenome property)

O

order_gene_lists() (in module ppanggolin.figures.draw_spot) order_nodes() (in module ppanggolin.figures.tile_plot) Organism (class in ppanggolin.genome) organism (ppanggolin.genome.Contig property) (ppanggolin.genome.Feature property) (ppanggolin.region.Region property) organism_desc() (in module ppanggolin.formats.writeAnnotations)

organisms (ppanggolin.edge.Edge property) (ppanggolin.geneFamily.GeneFamily property) (ppanggolin.pangenome.Pangenome property) (ppanggolin.region.Module property) overlap_filter() (in module ppanggolin.annotate.synta) overlaps_contig_edge (ppanggolin.genome.Feature property) (ppanggolin.region.Region property) overwrite_args() (in module ppanggolin.utils)

P

palette() (in module ppanggolin.formats.writeFlatGenomes) Pangenome (class in ppanggolin.pangenome) parse_config_file() (in module ppanggolin.utils) parse_contig_header_lines() (in module ppanggolin.annotate.annotate) parse_db_xref_metadata() (in module ppanggolin.annotate.annotate) parse_dna_seq_lines() (in module ppanggolin.annotate.annotate) parse_fasta() (in module ppanggolin.annotate.synta) parse_feature_lines() (in module ppanggolin.annotate.annotate) parse_gbff_by_contig() (in module ppanggolin.annotate.annotate) parse_input_paths_file() (in module ppanggolin.utils) parser_align() (in module ppanggolin.align.alignOnPang) parser_annot() (in module ppanggolin.annotate.annotate) parser_clust() (in module ppanggolin.cluster.cluster) parser_cluster_rgp() (in module ppanggolin.RGP.rgp_cluster) parser_context() (in module ppanggolin.context.searchGeneContext) parser_default_config() (in module ppanggolin.utility.utils) parser_draw() (in module ppanggolin.figures.drawing) parser_flat() (in module ppanggolin.formats.writeFlatGenomes) (in module ppanggolin.formats.writeFlatPangenome) parser_graph() (in module ppanggolin.graph.makeGraph) parser_info() (in module ppanggolin.info.info) parser_meta() (in module ppanggolin.meta.meta) parser_metrics() (in module ppanggolin.metrics.metrics) parser_module() (in module ppanggolin.mod.module) parser_msa() (in module ppanggolin.formats.writeMSA) parser_partition() (in module ppanggolin.nem.partition) parser_projection() (in module ppanggolin.projection.projection) parser_rarefaction() (in module ppanggolin.nem.rarefaction) parser_rgp() (in module ppanggolin.RGP.genomicIsland) parser_seq() (in module ppanggolin.formats.writeSequences) parser_spot() (in module ppanggolin.RGP.spot) partition (ppanggolin.geneFamily.GeneFamily property) partition() (in module ppanggolin.nem.partition) partition_nem() (in module ppanggolin.nem.partition) ppanggolin module ppanggolin.align module ppanggolin.align.alignOnPang module ppanggolin.annotate module ppanggolin.annotate.annotate module ppanggolin.annotate.synta module ppanggolin.cluster module ppanggolin.cluster.cluster module ppanggolin.context module ppanggolin.context.searchGeneContext module ppanggolin.edge module ppanggolin.figures module ppanggolin.figures.draw_spot module ppanggolin.figures.drawing module ppanggolin.figures.tile_plot module ppanggolin.figures.ucurve module ppanggolin.formats module ppanggolin.formats.readBinaries module ppanggolin.formats.write_proksee module ppanggolin.formats.writeAnnotations module ppanggolin.formats.writeBinaries module ppanggolin.formats.writeFlatGenomes module ppanggolin.formats.writeFlatPangenome module ppanggolin.formats.writeMetadata module ppanggolin.formats.writeMSA module

ppanggolin.formats.writeSequences module ppanggolin.geneFamily module ppanggolin.genetic_codes module ppanggolin.genome module ppanggolin.graph module ppanggolin.graph.makeGraph module ppanggolin.info module ppanggolin.info.info module ppanggolin.main module ppanggolin.meta module ppanggolin.meta.meta module ppanggolin.metadata module ppanggolin.metrics module ppanggolin.metrics.fluidity module ppanggolin.metrics.metrics module ppanggolin.mod module ppanggolin.mod.module module ppanggolin.nem module ppanggolin.nem.partition module ppanggolin.nem.rarefaction module ppanggolin.pangenome module ppanggolin.projection module ppanggolin.projection.projection module ppanggolin.region module ppanggolin.RGP module ppanggolin.RGP.genomicIsland module ppanggolin.RGP.rgp_cluster module ppanggolin.RGP.spot module ppanggolin.utility module ppanggolin.utility.utils module ppanggolin.utils module ppanggolin.workflow module ppanggolin.workflow.all module ppanggolin.workflow.panModule module ppanggolin.workflow.panRGP module ppanggolin.workflow.workflow module predict_hotspots() (in module ppanggolin.RGP.spot) predict_modules() (in module ppanggolin.mod.module) predict_RGP() (in module ppanggolin.projection.projection) predict_rgp() (in module ppanggolin.RGP.genomicIsland) predict_spot_in_one_organism() (in module ppanggolin.projection.projection) predict_spots_in_input_organisms() (in module ppanggolin.projection.projection) prepare_data_structures() (in module ppanggolin.figures.tile_plot) print_computed_metric() (in module ppanggolin.metrics.metrics) print_info() (in module ppanggolin.info.info) print_yaml() (in module ppanggolin.info.info) process_tile_data() (in module ppanggolin.figures.tile_plot) project_and_write_modules() (in module ppanggolin.projection.projection) project_and_write_partition() (in module ppanggolin.align.alignOnPang)

R

raref_nem() (in module ppanggolin.nem.rarefaction) read_anno_file() (in module ppanggolin.annotate.annotate) read_annotation() (in module ppanggolin.formats.readBinaries) read_annotation_files() (in module ppanggolin.projection.projection) read_annotations() (in module ppanggolin.annotate.annotate) read_chunks() (in module ppanggolin.formats.readBinaries) read_clustering() (in module ppanggolin.cluster.cluster) read_clustering_file() (in module ppanggolin.cluster.cluster) read_compressed_or_not() (in module ppanggolin.utils) read_contigs() (in module ppanggolin.formats.readBinaries) read_faa() (in module ppanggolin.cluster.cluster) read_fam2seq() (in module ppanggolin.cluster.cluster) read_fasta_gbk() (in module ppanggolin.formats.writeSequences) read_fasta_or_gff() (in module ppanggolin.formats.writeSequences) read_gene2fam() (in module ppanggolin.cluster.cluster) read_gene_families() (in module ppanggolin.formats.readBinaries) read_gene_families_info() (in module ppanggolin.formats.readBinaries) read_gene_sequences() (in module ppanggolin.formats.readBinaries) read_genedata() (in module ppanggolin.formats.readBinaries) read_genes() (in module ppanggolin.formats.readBinaries) read_genome_file() (in module ppanggolin.formats.writeSequences) read_graph() (in module ppanggolin.formats.readBinaries) read_info() (in module ppanggolin.formats.readBinaries) read_join_coordinates() (in module ppanggolin.formats.readBinaries) read_metadata() (in module ppanggolin.formats.readBinaries) read_metadata_status() (in module ppanggolin.info.info) read_module_families_from_pangenome_file() (in module ppanggolin.formats.readBinaries) read_modules() (in module ppanggolin.formats.readBinaries) read_org_gbff() (in module ppanggolin.annotate.annotate) read_org_gff() (in module ppanggolin.annotate.annotate) read_organisms() (in module ppanggolin.formats.readBinaries) read_pangenome() (in module ppanggolin.formats.readBinaries) read_parameters() (in module ppanggolin.formats.readBinaries) read_rgp() (in module ppanggolin.formats.readBinaries) read_rgp_genes_from_pangenome_file() (in module ppanggolin.formats.readBinaries)

read_rnas() (in module ppanggolin.formats.readBinaries) read_sequences() (in module ppanggolin.formats.readBinaries) read_spots() (in module ppanggolin.formats.readBinaries) read_status() (in module ppanggolin.info.info) read_tsv() (in module ppanggolin.cluster.cluster) refine_clustering() (in module ppanggolin.cluster.cluster) Region (class in ppanggolin.region) regions (ppanggolin.genome.Contig property) (ppanggolin.genome.Organism property) (ppanggolin.pangenome.Pangenome property) (ppanggolin.region.Spot property) remove() (ppanggolin.geneFamily.GeneFamily method) (ppanggolin.genome.Contig method) (ppanggolin.genome.Organism method) (ppanggolin.region.Module method) (ppanggolin.region.Region method) (ppanggolin.region.Spot method) remove_high_copy_number() (in module ppanggolin.graph.makeGraph) replace_non_ascii() (in module ppanggolin.utils) representative (ppanggolin.geneFamily.GeneFamily property) restricted_float() (in module ppanggolin.utils) retrieve_gene_sequences_from_fasta_file() (in module ppanggolin.projection.projection) reverse_complement() (in module ppanggolin.annotate.synta) reverse_complement_coordinates() (in module ppanggolin.annotate.annotate) rewrite_matrix() (in module ppanggolin.RGP.genomicIsland) RGP (ppanggolin.genome.Gene property) rgp_desc() (in module ppanggolin.formats.writeBinaries) RNA (class in ppanggolin.genome) rna_desc() (in module ppanggolin.formats.writeAnnotations) rna_genes (ppanggolin.genome.Organism property) RNAs (ppanggolin.genome.Contig property) (ppanggolin.pangenome.Pangenome property) row_order_gene_lists() (in module ppanggolin.figures.draw_spot) run_partitioning() (in module ppanggolin.nem.partition) run_subprocess() (in module ppanggolin.utils)

S

search_gene_context_in_pangenome() (in module ppanggolin.context.searchGeneContext) select_elem() (ppanggolin.pangenome.Pangenome method) sequence_desc() (in module ppanggolin.formats.writeAnnotations) set_edge() (ppanggolin.geneFamily.GeneFamily method) set_module() (ppanggolin.geneFamily.GeneFamily method) set_up_config_param_to_parser() (in module ppanggolin.utils) set_verbosity_level() (in module ppanggolin.utils) shift_end_coordinates() (in module ppanggolin.annotate.annotate) shift_start_coordinates() (in module ppanggolin.annotate.annotate) soft_core_families() (ppanggolin.pangenome.Pangenome method) sources (ppanggolin.metadata.MetaFeatures property) split() (in module ppanggolin.utility.utils) split_comment_string() (in module ppanggolin.utility.utils) Spot (class in ppanggolin.region) spot (ppanggolin.genome.Gene property) (ppanggolin.region.Region property) spot2rgp() (in module ppanggolin.formats.writeFlatPangenome) spot_2_families() (ppanggolin.region.Spot method) spot_desc() (in module ppanggolin.formats.writeBinaries) spots (ppanggolin.geneFamily.GeneFamily property) (ppanggolin.genome.Contig property) (ppanggolin.genome.Organism property) (ppanggolin.pangenome.Pangenome property) (ppanggolin.RGP.rgp_cluster.IdenticalRegions property) start (ppanggolin.region.Region property) start_relative_to() (ppanggolin.genome.Feature method) starter (ppanggolin.region.Region property) stop (ppanggolin.region.Region property) stop_relative_to() (ppanggolin.genome.Feature method) stopper (ppanggolin.region.Region property) string_coordinates() (ppanggolin.genome.Feature method) (ppanggolin.region.Region method)

subgraph() (in module ppanggolin.figures.draw_spot) subparser() (in module ppanggolin.align.alignOnPang) (in module ppanggolin.annotate.annotate) (in module ppanggolin.cluster.cluster) (in module ppanggolin.context.searchGeneContext) (in module ppanggolin.figures.drawing) (in module ppanggolin.formats.writeFlatGenomes) (in module ppanggolin.formats.writeFlatPangenome) (in module ppanggolin.formats.writeMSA) (in module ppanggolin.formats.writeSequences) (in module ppanggolin.graph.makeGraph) (in module ppanggolin.info.info) (in module ppanggolin.meta.meta) (in module ppanggolin.metrics.metrics) (in module ppanggolin.mod.module) (in module ppanggolin.nem.partition) (in module ppanggolin.nem.rarefaction) (in module ppanggolin.projection.projection) (in module ppanggolin.RGP.genomicIsland) (in module ppanggolin.RGP.rgp_cluster) (in module ppanggolin.RGP.spot) (in module ppanggolin.utility.utils) (in module ppanggolin.workflow.all) (in module ppanggolin.workflow.panModule) (in module ppanggolin.workflow.panRGP) (in module ppanggolin.workflow.workflow) summarize_genome() (in module ppanggolin.formats.writeFlatPangenome) summarize_projected_genome() (in module ppanggolin.projection.projection) summarize_spots() (in module ppanggolin.formats.writeFlatPangenome) syntaxic_annotation() (in module ppanggolin.annotate.synta)

T

to_dict() (ppanggolin.metadata.Metadata method)

translate() (in module ppanggolin.formats.writeMSA) translate_genes() (in module ppanggolin.formats.writeSequences)

U

update_gene_fam_partition() (in module ppanggolin.formats.writeBinaries)

update_gene_fragments() (in module ppanggolin.formats.writeBinaries)

W

write_all_gene_sequences() (in module ppanggolin.align.alignOnPang) write_annotations() (in module ppanggolin.formats.writeAnnotations) write_borders() (in module ppanggolin.formats.writeFlatPangenome) write_compressed_or_not() (in module ppanggolin.utils) write_contig() (in module ppanggolin.formats.write_proksee) write_contigs() (in module ppanggolin.formats.writeAnnotations) write_fasta_families() (in module ppanggolin.formats.writeMSA) write_fasta_gene_fam_from_pangenome_file() (in module ppanggolin.formats.readBinaries) write_fasta_prot_fam_from_pangenome_file() (in module ppanggolin.formats.readBinaries) write_flat_genome_files() (in module ppanggolin.formats.writeFlatGenomes) write_gene_fam_info() (in module ppanggolin.formats.writeBinaries) write_gene_fam_sequences() (in module ppanggolin.align.alignOnPang) write_gene_families() (in module ppanggolin.formats.writeBinaries) write_gene_families_tsv() (in module ppanggolin.formats.writeFlatPangenome) write_gene_joined_coordinates() (in module ppanggolin.formats.writeAnnotations) write_gene_presence_absence() (in module ppanggolin.formats.writeFlatPangenome) write_gene_protein_sequences() (in module ppanggolin.formats.writeSequences) write_gene_sequences() (in module ppanggolin.formats.writeAnnotations) write_gene_sequences_from_annotations() (in module ppanggolin.formats.writeSequences) write_gene_sequences_from_pangenome_file() (in module ppanggolin.formats.readBinaries) write_gene_to_gene_family() (in module ppanggolin.align.alignOnPang) write_genedata() (in module ppanggolin.formats.writeAnnotations) write_genes() (in module ppanggolin.formats.write_proksee) (in module ppanggolin.formats.writeAnnotations) write_genes_from_pangenome_file() (in module ppanggolin.formats.readBinaries) write_genes_seq_from_pangenome_file() (in module ppanggolin.formats.readBinaries) write_gexf() (in module ppanggolin.formats.writeFlatPangenome) write_gexf_edges() (in module ppanggolin.formats.writeFlatPangenome) write_gexf_end() (in module ppanggolin.formats.writeFlatPangenome) write_gexf_header() (in module ppanggolin.formats.writeFlatPangenome) write_gexf_nodes() (in module ppanggolin.formats.writeFlatPangenome) write_gff_file() (in module ppanggolin.formats.writeFlatGenomes) write_graph() (in module ppanggolin.context.searchGeneContext) (in module ppanggolin.formats.writeBinaries) write_info() (in module ppanggolin.formats.writeBinaries) write_info_modules() (in module ppanggolin.formats.writeBinaries) write_json() (in module ppanggolin.formats.writeFlatPangenome) write_json_edge() (in module ppanggolin.formats.writeFlatPangenome) write_json_edges() (in module ppanggolin.formats.writeFlatPangenome) write_json_gene_fam() (in module ppanggolin.formats.writeFlatPangenome) write_json_header() (in module ppanggolin.formats.writeFlatPangenome) write_json_nodes() (in module ppanggolin.formats.writeFlatPangenome) write_legend_items() (in module ppanggolin.formats.write_proksee) write_matrix() (in module ppanggolin.formats.writeFlatPangenome)

write_metadata() (in module ppanggolin.formats.writeMetadata) write_metadata_contig() (in module ppanggolin.formats.writeMetadata) write_metadata_group() (in module ppanggolin.formats.writeMetadata) write_metadata_metatype() (in module ppanggolin.formats.writeMetadata) write_metadata_status() (in module ppanggolin.formats.writeMetadata) write_metrics() (in module ppanggolin.metrics.metrics) write_module_summary() (in module ppanggolin.formats.writeFlatPangenome) write_modules() (in module ppanggolin.formats.write_proksee) (in module ppanggolin.formats.writeBinaries) (in module ppanggolin.formats.writeFlatPangenome) write_msa_files() (in module ppanggolin.formats.writeMSA) write_nem_input_files() (in module ppanggolin.nem.partition) write_org_modules() (in module ppanggolin.formats.writeFlatPangenome) write_organisms() (in module ppanggolin.formats.writeAnnotations) write_pangenome() (in module ppanggolin.formats.writeBinaries) write_pangenome_flat_files() (in module ppanggolin.formats.writeFlatPangenome) write_partitions() (in module ppanggolin.formats.writeFlatPangenome) write_persistent_duplication_statistics() (in module ppanggolin.formats.writeFlatPangenome) write_projection_results() (in module ppanggolin.projection.projection) write_proksee_organism() (in module ppanggolin.formats.write_proksee) write_regions() (in module ppanggolin.formats.writeFlatPangenome) write_regions_families() (in module ppanggolin.formats.writeFlatPangenome) write_regions_sequences() (in module ppanggolin.formats.writeSequences) write_rgp() (in module ppanggolin.formats.write_proksee) (in module ppanggolin.formats.writeBinaries) write_rgp_cluster_table() (in module ppanggolin.RGP.rgp_cluster) write_rgp_modules() (in module ppanggolin.formats.writeFlatPangenome) write_rgp_table() (in module ppanggolin.formats.writeFlatPangenome) write_rgp_to_spot_table() (in module ppanggolin.projection.projection) write_rnas() (in module ppanggolin.formats.writeAnnotations) write_sequence_files() (in module ppanggolin.formats.writeSequences) write_spaced_fasta() (in module ppanggolin.formats.writeSequences) write_spot_graph() (in module ppanggolin.RGP.spot) write_spot_modules() (in module ppanggolin.formats.writeFlatPangenome) write_spots() (in module ppanggolin.formats.writeBinaries) (in module ppanggolin.formats.writeFlatPangenome) write_stats() (in module ppanggolin.formats.writeFlatPangenome) write_status() (in module ppanggolin.formats.writeBinaries) write_summaries_in_tsv() (in module ppanggolin.formats.writeFlatPangenome) write_summary_in_yaml() (in module ppanggolin.projection.projection) write_tmp_fasta() (in module ppanggolin.annotate.synta) write_tracks() (in module ppanggolin.formats.write_proksee) write_tsv_genome_file() (in module ppanggolin.formats.writeFlatGenomes) write_whole_genome_msa() (in module ppanggolin.formats.writeMSA)