Index

A

add_missing_genomes() (in module PanACoTA.align_module.alignment) align_all_families() (in module PanACoTA.align_module.alignment)

analyse_all_genomes() (in module PanACoTA.annotate_module.genome_seq_functions) analyse_genome() (in module PanACoTA.annotate_module.genome_seq_functions)

B

back_translate() (in module PanACoTA.align_module.alignment) build_parser() (in module PanACoTA.subcommands.align) (in module PanACoTA.subcommands.all_modules) (in module PanACoTA.subcommands.annotate) (in module PanACoTA.subcommands.corepers) (in module PanACoTA.subcommands.pangenome) (in module PanACoTA.subcommands.prepare) (in module PanACoTA.subcommands.tree)

build_prt_bank() (in module PanACoTA.pangenome_module.protein_seq_functions)

C

calc_l90() (in module PanACoTA.annotate_module.genome_seq_functions) cat() (in module PanACoTA.utils) check_add_missing() (in module PanACoTA.align_module.alignment) check_args() (in module PanACoTA.subcommands.all_modules) (in module PanACoTA.subcommands.annotate) (in module PanACoTA.subcommands.corepers) (in module PanACoTA.subcommands.prepare) (in module PanACoTA.subcommands.tree) check_existing_extract() (in module PanACoTA.align_module.get_seqs) check_extractions() (in module PanACoTA.align_module.alignment) check_format() (in module PanACoTA.utils) check_installed() (in module PanACoTA.utils) check_lens() (in module PanACoTA.align_module.alignment) check_nb_seqs() (in module PanACoTA.align_module.alignment) check_out_dirs() (in module PanACoTA.utils) check_prodigal() (in module PanACoTA.annotate_module.annotation_functions)

check_prokka() (in module PanACoTA.annotate_module.annotation_functions) check_quality() (in module PanACoTA.prepare_module.filter_genomes) clusters_to_file() (in module PanACoTA.pangenome_module.mmseqs_functions) compare_all() (in module PanACoTA.prepare_module.filter_genomes) concat_alignments() (in module PanACoTA.align_module.post_align) convert2phylip() (in module PanACoTA.tree_module.fastme_func) convert2stockholm() (in module PanACoTA.tree_module.quicktree_func) count() (in module PanACoTA.utils) count_headers() (in module PanACoTA.annotate_module.annotation_functions) count_tbl() (in module PanACoTA.annotate_module.annotation_functions) create_gen() (in module PanACoTA.annotate_module.format_prokka) create_gene_lst() (in module PanACoTA.annotate_module.format_prodigal) create_gff() (in module PanACoTA.annotate_module.format_prodigal) create_mmseqs_db() (in module PanACoTA.pangenome_module.mmseqs_functions) create_prt() (in module PanACoTA.annotate_module.format_prodigal) (in module PanACoTA.annotate_module.format_prokka)

D

define_nb_threads() (in module PanACoTA.tree_module.fasttree_func) detail_lvl() (in module PanACoTA.utils)

do_mmseqs_db() (in module PanACoTA.pangenome_module.mmseqs_functions) do_pangenome() (in module PanACoTA.pangenome_module.mmseqs_functions) download_from_ncbi() (in module PanACoTA.prepare_module.download_genomes_func)

E

extract_sequences() (in module PanACoTA.align_module.get_seqs)

F

family_alignment() (in module PanACoTA.align_module.alignment) filter() (PanACoTA.utils.LessThanFilter method) (PanACoTA.utils.NoLevelFilter method)

format_contig() (in module PanACoTA.annotate_module.genome_seq_functions) format_genomes() (in module PanACoTA.annotate_module.general_format_functions) format_one_genome() (in module PanACoTA.annotate_module.format_prodigal) (in module PanACoTA.annotate_module.format_prokka)

G

generate_and_write_outputs() (in module PanACoTA.pangenome_module.post_treatment) generate_gff() (in module PanACoTA.annotate_module.format_prokka) get_align() (in module PanACoTA.subcommands.all_modules) get_all_genomes() (in module PanACoTA.align_module.pan_to_pergenome) get_all_seqs() (in module PanACoTA.align_module.get_seqs) get_annotate() (in module PanACoTA.subcommands.all_modules) get_corepers() (in module PanACoTA.subcommands.all_modules) get_fams_info() (in module PanACoTA.utils_pangenome) get_genome() (in module PanACoTA.align_module.post_align) get_genome_contigs_and_rename() (in module PanACoTA.utils) get_genome_seqs() (in module PanACoTA.align_module.get_seqs) get_info() (in module PanACoTA.pangenome_module.mmseqs_functions) (in module PanACoTA.subcommands.corepers)

get_logmmseq() (in module PanACoTA.pangenome_module.mmseqs_functions) get_names_to_extract() (in module PanACoTA.align_module.get_seqs) get_output_dir() (in module PanACoTA.annotate_module.genome_seq_functions) get_pangenome() (in module PanACoTA.subcommands.all_modules) get_per_genome() (in module PanACoTA.align_module.pan_to_pergenome) get_pers() (in module PanACoTA.corepers_module.persistent_functions) get_prepare() (in module PanACoTA.subcommands.all_modules) get_subset_genomes() (in module PanACoTA.corepers_module.persistent_functions) get_tree() (in module PanACoTA.subcommands.all_modules) grep() (in module PanACoTA.utils) group_by_genome() (in module PanACoTA.align_module.post_align)

H

handle_family() (in module PanACoTA.align_module.alignment)

handle_family_1thread() (in module PanACoTA.align_module.alignment) handle_genome() (in module PanACoTA.annotate_module.general_format_functions)

I

init_logger() (in module PanACoTA.utils)

is_in_subset() (in module PanACoTA.corepers_module.persistent_functions) iterative_mash() (in module PanACoTA.prepare_module.filter_genomes)

L

launch_group_by_genome() (in module PanACoTA.align_module.post_align) LessThanFilter (class in PanACoTA.utils)

list_to_str() (in module PanACoTA.utils) load_bin() (in module PanACoTA.utils) logger_thread() (in module PanACoTA.utils)

M

mafft_align() (in module PanACoTA.align_module.alignment) main() (in module PanACoTA.subcommands.align) (in module PanACoTA.subcommands.all_modules) (in module PanACoTA.subcommands.annotate) (in module PanACoTA.subcommands.corepers) (in module PanACoTA.subcommands.pangenome) (in module PanACoTA.subcommands.prepare) (in module PanACoTA.subcommands.tree) main_from_parse() (in module PanACoTA.subcommands.align) (in module PanACoTA.subcommands.all_modules) (in module PanACoTA.subcommands.annotate) (in module PanACoTA.subcommands.corepers) (in module PanACoTA.subcommands.pangenome) (in module PanACoTA.subcommands.prepare) (in module PanACoTA.subcommands.tree) mash_step() (in module PanACoTA.prepare_module.filter_genomes) mixed_family() (in module PanACoTA.corepers_module.persistent_functions) mmseq_tsv_to_clusters() (in module PanACoTA.pangenome_module.mmseqs_functions) mmseqs_to_pangenome() (in module PanACoTA.pangenome_module.mmseqs_functions) mmseqs_tsv_to_pangenome() (in module PanACoTA.pangenome_module.mmseqs_functions) module PanACoTA.align_module.alignment PanACoTA.align_module.get_seqs PanACoTA.align_module.pan_to_pergenome PanACoTA.align_module.post_align PanACoTA.annotate_module PanACoTA.annotate_module.annotation_functions PanACoTA.annotate_module.format_prodigal PanACoTA.annotate_module.format_prokka PanACoTA.annotate_module.general_format_functions PanACoTA.annotate_module.genome_seq_functions PanACoTA.corepers_module PanACoTA.corepers_module.persistent_functions PanACoTA.pangenome_module PanACoTA.pangenome_module.mmseqs_functions PanACoTA.pangenome_module.post_treatment PanACoTA.pangenome_module.protein_seq_functions PanACoTA.prepare_module PanACoTA.prepare_module.download_genomes_func PanACoTA.prepare_module.filter_genomes PanACoTA.subcommands PanACoTA.subcommands.align PanACoTA.subcommands.all_modules PanACoTA.subcommands.annotate PanACoTA.subcommands.corepers PanACoTA.subcommands.pangenome PanACoTA.subcommands.prepare PanACoTA.subcommands.tree PanACoTA.tree_module PanACoTA.tree_module.fastme_func PanACoTA.tree_module.fasttree_func PanACoTA.tree_module.quicktree_func PanACoTA.utils PanACoTA.utils_pangenome

N

NoLevelFilter (class in PanACoTA.utils)

O

open_outputs_to_write() (in module PanACoTA.pangenome_module.post_treatment)

P

PanACoTA.align_module.alignment module PanACoTA.align_module.get_seqs module PanACoTA.align_module.pan_to_pergenome module PanACoTA.align_module.post_align module PanACoTA.annotate_module module PanACoTA.annotate_module.annotation_functions module PanACoTA.annotate_module.format_prodigal module PanACoTA.annotate_module.format_prokka module PanACoTA.annotate_module.general_format_functions module PanACoTA.annotate_module.genome_seq_functions module PanACoTA.corepers_module module PanACoTA.corepers_module.persistent_functions module PanACoTA.pangenome_module module PanACoTA.pangenome_module.mmseqs_functions module PanACoTA.pangenome_module.post_treatment module PanACoTA.pangenome_module.protein_seq_functions module PanACoTA.prepare_module module PanACoTA.prepare_module.download_genomes_func module PanACoTA.prepare_module.filter_genomes module PanACoTA.subcommands module

PanACoTA.subcommands.align module PanACoTA.subcommands.all_modules module PanACoTA.subcommands.annotate module PanACoTA.subcommands.corepers module PanACoTA.subcommands.pangenome module PanACoTA.subcommands.prepare module PanACoTA.subcommands.tree module PanACoTA.tree_module module PanACoTA.tree_module.fastme_func module PanACoTA.tree_module.fasttree_func module PanACoTA.tree_module.quicktree_func module PanACoTA.utils module PanACoTA.utils_pangenome module parse() (in module PanACoTA.subcommands.align) (in module PanACoTA.subcommands.all_modules) (in module PanACoTA.subcommands.annotate) (in module PanACoTA.subcommands.corepers) (in module PanACoTA.subcommands.pangenome) (in module PanACoTA.subcommands.prepare) (in module PanACoTA.subcommands.tree) plot_distr() (in module PanACoTA.utils) plot_distributions() (in module PanACoTA.annotate_module.genome_seq_functions) post_alignment() (in module PanACoTA.align_module.post_align) post_treat() (in module PanACoTA.pangenome_module.post_treatment) prodigal_train() (in module PanACoTA.annotate_module.annotation_functions) proteins_per_strain() (in module PanACoTA.align_module.pan_to_pergenome)

R

read_alignments() (in module PanACoTA.align_module.post_align) read_gene() (in module PanACoTA.utils_pangenome) read_genomes() (in module PanACoTA.utils) read_genomes_info() (in module PanACoTA.utils) read_info() (in module PanACoTA.utils) read_lstinfo() (in module PanACoTA.utils_pangenome) read_matrix() (in module PanACoTA.prepare_module.filter_genomes) read_pan_file() (in module PanACoTA.utils_pangenome) read_pangenome() (in module PanACoTA.utils_pangenome) remove() (in module PanACoTA.utils) rename_all_genomes() (in module PanACoTA.annotate_module.genome_seq_functions)

run_all_pangenome() (in module PanACoTA.pangenome_module.mmseqs_functions) run_annotation_all() (in module PanACoTA.annotate_module.annotation_functions) run_cmd() (in module PanACoTA.utils) run_fastme() (in module PanACoTA.tree_module.fastme_func) run_fasttree() (in module PanACoTA.tree_module.fasttree_func) run_mmseqs_clust() (in module PanACoTA.pangenome_module.mmseqs_functions) run_prodigal() (in module PanACoTA.annotate_module.annotation_functions) run_prokka() (in module PanACoTA.annotate_module.annotation_functions) run_quicktree() (in module PanACoTA.tree_module.quicktree_func) run_tree() (in module PanACoTA.tree_module.fastme_func) (in module PanACoTA.tree_module.fasttree_func) (in module PanACoTA.tree_module.quicktree_func)

S

save_bin() (in module PanACoTA.utils) sketch_all() (in module PanACoTA.prepare_module.filter_genomes) sort_genomes_by_name() (in module PanACoTA.utils) sort_genomes_byname_l90_nbcont() (in module PanACoTA.utils)

sort_genomes_l90_nbcont() (in module PanACoTA.utils) sort_genomes_minhash() (in module PanACoTA.prepare_module.filter_genomes) sort_proteins() (in module PanACoTA.utils) split_contig() (in module PanACoTA.annotate_module.genome_seq_functions)

T

tbl2lst() (in module PanACoTA.annotate_module.format_prokka)

thread_progressbar() (in module PanACoTA.utils) to_database() (in module PanACoTA.prepare_module.download_genomes_func)

U

uniq_members() (in module PanACoTA.corepers_module.persistent_functions)

W

write_gene() (in module PanACoTA.annotate_module.general_format_functions) write_genome_file() (in module PanACoTA.align_module.pan_to_pergenome) write_genomes_info() (in module PanACoTA.utils) write_getentry_files() (in module PanACoTA.align_module.pan_to_pergenome) write_groups() (in module PanACoTA.align_module.post_align) write_header() (in module PanACoTA.annotate_module.general_format_functions)

write_list() (in module PanACoTA.utils) write_lstinfo() (in module PanACoTA.utils) write_missing_genomes() (in module PanACoTA.align_module.pan_to_pergenome) write_outputfiles() (in module PanACoTA.prepare_module.filter_genomes) write_persistent() (in module PanACoTA.corepers_module.persistent_functions) write_warning_skipped() (in module PanACoTA.utils)