Index

_

__init__() (cladeomatic.clades.clade_worker method) (cladeomatic.kmers.kmer_worker method)

A

as_range() (cladeomatic.clades.clade_worker method)

C

calc_AMI() (in module cladeomatic.utils.__init__) calc_ARI() (in module cladeomatic.utils.__init__) calc_consensus_seq() (cladeomatic.kmers.kmer_worker method) calc_homopolymers() (in module cladeomatic.utils.seqdata) calc_md5() (in module cladeomatic.utils.seqdata) calc_metadata_counts() (cladeomatic.clades.clade_worker method) calc_node_associations_groups() (cladeomatic.clades.clade_worker method) calc_node_distances() (cladeomatic.clades.clade_worker method) calc_shanon_entropy() (in module cladeomatic.utils.__init__) check_file() (cladeomatic.utils.vcfhelper.vcfReader method) check_nodes() (cladeomatic.clades.clade_worker method) clade_snp_association() (cladeomatic.clades.clade_worker method) clade_snp_count() (cladeomatic.clades.clade_worker method) clade_worker (class in cladeomatic.clades) cladeomatic.benchmark module cladeomatic.clades module cladeomatic.constants module cladeomatic.genotype module cladeomatic.kmers module cladeomatic.main module cladeomatic.namer module cladeomatic.snps module

cladeomatic.utils.__init__ module cladeomatic.utils.jellyfish module cladeomatic.utils.kmerSearch module cladeomatic.utils.seqdata module cladeomatic.utils.snpdists module cladeomatic.utils.vcfhelper module cladeomatic.utils.visualization module cladeomatic.visualize module cladeomatic.writers module compress_heirarchy() (cladeomatic.clades.clade_worker method) compression_cleanup() (cladeomatic.clades.clade_worker method) confirm_kmer_specificity() (cladeomatic.kmers.kmer_worker method) construct_ruleset() (cladeomatic.kmers.kmer_worker method) convert_features_to_mutations() (in module cladeomatic.genotype) convert_genotype_report() (in module cladeomatic.benchmark) create_aln_pos_from_unalign_pos_lookup() (in module cladeomatic.utils.seqdata) create_biohansel_kmers() (cladeomatic.kmers.kmer_worker method) create_cluster_membership_lookup() (cladeomatic.clades.clade_worker method) create_dist_histo() (in module cladeomatic.utils.visualization) create_pseudoseqs_from_vcf() (in module cladeomatic.utils.seqdata)

D

dist_based_nomenclature() (cladeomatic.clades.clade_worker method)

distance_node_binning() (cladeomatic.clades.clade_worker method)

E

expand_degenerate_bases() (in module cladeomatic.utils.kmerSearch)

extract_kmers() (cladeomatic.kmers.kmer_worker method)

F

filter_genotypes_exclude() (in module cladeomatic.benchmark) filter_genotypes_include() (in module cladeomatic.benchmark) find_dist_troughs() (cladeomatic.clades.clade_worker method) find_invalid_kmers() (cladeomatic.kmers.kmer_worker method)

find_variant_positions() (cladeomatic.kmers.kmer_worker method) fit_clusters_to_groupings() (cladeomatic.clades.clade_worker method) fix_root() (cladeomatic.clades.clade_worker method) flag_invalid_kmers() (cladeomatic.kmers.kmer_worker method)

G

gb_to_fasta_dict() (in module cladeomatic.utils.seqdata) generate_genotypes() (cladeomatic.clades.clade_worker method) generate_non_gap_position_lookup() (in module cladeomatic.utils.seqdata) genotype_lookup() (cladeomatic.clades.clade_worker method) get_all_nodes() (cladeomatic.clades.clade_worker method) get_bifurcating_nodes() (cladeomatic.clades.clade_worker method) get_clade_distances() (cladeomatic.clades.clade_worker method) get_close_nodes() (cladeomatic.clades.clade_worker method) get_conserved_ranges() (cladeomatic.clades.clade_worker method) get_genotype_counts() (in module cladeomatic.benchmark) get_genotype_snp_rules() (cladeomatic.clades.clade_worker method) get_genotype_snp_states() (cladeomatic.kmers.kmer_worker method) get_inter_clade_distances() (cladeomatic.clades.clade_worker method)

get_kseq_by_index() (cladeomatic.kmers.kmer_worker method) get_largest_conserved_pos() (cladeomatic.clades.clade_worker method) get_node_member_counts() (cladeomatic.clades.clade_worker method) get_optimal_kmer_position() (cladeomatic.kmers.kmer_worker method) get_pos_without_kmer() (cladeomatic.kmers.kmer_worker method) get_problem_bases() (in module cladeomatic.benchmark) get_selected_nodes() (cladeomatic.clades.clade_worker method) get_selected_positions() (cladeomatic.clades.clade_worker method) get_snp_profiles() (in module cladeomatic.genotype) get_terminal_nodes() (cladeomatic.clades.clade_worker method) get_valid_nodes() (cladeomatic.clades.clade_worker method) get_variant_positions() (cladeomatic.clades.clade_worker method) get_variants() (in module cladeomatic.utils.seqdata)

I

identify_dist_ranges() (cladeomatic.clades.clade_worker method) init_automaton_dict() (in module cladeomatic.utils.kmerSearch) init_clade_data() (cladeomatic.clades.clade_worker method)

init_console_logger() (in module cladeomatic.utils.__init__) init_kmer_scheme_data() (cladeomatic.kmers.kmer_worker method) init_msa_base_counts() (cladeomatic.kmers.kmer_worker method) is_valid_file() (in module cladeomatic.genotype)

K

kmer_worker (class in cladeomatic.kmers)

M

module cladeomatic.benchmark cladeomatic.clades cladeomatic.constants cladeomatic.genotype cladeomatic.kmers cladeomatic.main cladeomatic.namer cladeomatic.snps cladeomatic.utils.__init__ cladeomatic.utils.jellyfish cladeomatic.utils.kmerSearch cladeomatic.utils.seqdata cladeomatic.utils.snpdists cladeomatic.utils.vcfhelper cladeomatic.utils.visualization cladeomatic.visualize cladeomatic.writers

N

next_row() (cladeomatic.utils.vcfhelper.vcfReader method)

P

parse_args() (in module cladeomatic.benchmark) (in module cladeomatic.genotype) (in module cladeomatic.namer) parse_genotype_report() (in module cladeomatic.benchmark) parse_metadata() (in module cladeomatic.utils.__init__) parse_reference_gbk() (in module cladeomatic.utils.seqdata) parse_scheme_features() (in module cladeomatic.genotype) parse_scheme_genotypes() (in module cladeomatic.genotype) partition_distances() (cladeomatic.clades.clade_worker method) perform_clustering() (cladeomatic.clades.clade_worker method) perform_kmer_search() (cladeomatic.kmers.kmer_worker method)

plot_bar() (in module cladeomatic.utils.visualization) pop_msa_base_counts() (cladeomatic.kmers.kmer_worker method) populate_clade_data() (cladeomatic.clades.clade_worker method) populate_int_base_kmer_lookup() (cladeomatic.kmers.kmer_worker method) populate_kmer_scheme_data() (cladeomatic.kmers.kmer_worker method) print_params() (in module cladeomatic.writers) print_usage_and_exit() (in module cladeomatic.main) process_kmer_results() (cladeomatic.kmers.kmer_worker method) process_row() (cladeomatic.utils.vcfhelper.vcfReader method) process_snp() (in module cladeomatic.snps) prune_snps() (cladeomatic.clades.clade_worker method)

R

read_fasta_dict() (in module cladeomatic.utils.seqdata) refine_rules() (cladeomatic.kmers.kmer_worker method) remove_empty_base_states() (cladeomatic.kmers.kmer_worker method) remove_invalid_kmers_from_scheme() (cladeomatic.kmers.kmer_worker method) remove_redundant_kmers() (cladeomatic.kmers.kmer_worker method) remove_scheme_pos() (cladeomatic.kmers.kmer_worker method) remove_snps() (cladeomatic.clades.clade_worker method)

rename() (in module cladeomatic.namer) revcomp() (in module cladeomatic.utils.kmerSearch) (in module cladeomatic.utils.seqdata) run() (in module cladeomatic.benchmark) (in module cladeomatic.genotype) (in module cladeomatic.namer) run_command() (in module cladeomatic.utils.__init__) run_snpdists() (in module cladeomatic.utils.snpdists)

S

SeqSearchController() (in module cladeomatic.utils.kmerSearch) set_genotype_snp_rules() (cladeomatic.clades.clade_worker method) set_genotype_snp_states() (cladeomatic.clades.clade_worker method) set_invalid_nodes() (cladeomatic.clades.clade_worker method)

set_valid_nodes() (cladeomatic.clades.clade_worker method) snp_based_filter() (cladeomatic.clades.clade_worker method) snp_search_controller() (in module cladeomatic.snps) summarize_snps() (cladeomatic.clades.clade_worker method)

T

temporal_signal() (cladeomatic.clades.clade_worker method)

U

update() (cladeomatic.clades.clade_worker method)

V

vcfReader (class in cladeomatic.utils.vcfhelper)

W

workflow() (cladeomatic.clades.clade_worker method) (cladeomatic.kmers.kmer_worker method) write_genotype_calls() (in module cladeomatic.genotype) write_genotypes() (in module cladeomatic.writers) write_kmers() (in module cladeomatic.writers)

write_node_report() (in module cladeomatic.writers) write_scheme() (in module cladeomatic.writers) write_scheme_scores() (in module cladeomatic.benchmark) write_snp_report() (in module cladeomatic.writers) write_updated_genotype_report() (in module cladeomatic.benchmark)