Index

A

as_dict() (cfoldseeker.classes.Cluster method) (cfoldseeker.classes.Hit method)

C

cfoldseeker.build_cds_db module cfoldseeker.classes module cfoldseeker.communication module cfoldseeker.extract_sequences module cfoldseeker.local module cfoldseeker.local_clustered module cfoldseeker.main module cfoldseeker.remote module cfoldseeker.remote_parsers module

check_duplicate_contigs() (in module cfoldseeker.build_cds_db) check_query_status() (in module cfoldseeker.communication) Cluster (class in cfoldseeker.classes) clusters (cfoldseeker.classes.Search attribute) collect_hits() (cfoldseeker.local.LocalSearch method) convert_session() (in module cfoldseeker.extract_sequences) coord_db (cfoldseeker.local.LocalSearch attribute) (cfoldseeker.local_clustered.LocalClusteredSearch attribute) coords (cfoldseeker.classes.Hit attribute) create_parser() (in module cfoldseeker.build_cds_db) (in module cfoldseeker.extract_sequences) (in module cfoldseeker.main) crossref_afdb() (cfoldseeker.remote.RemoteSearch method) crossref_afdb_via_genpept() (cfoldseeker.remote.RemoteSearch method) crossref_afdb_via_kegg() (cfoldseeker.remote.RemoteSearch method) crossref_afdb_via_wgs_genpept() (cfoldseeker.remote.RemoteSearch method) crossref_id (cfoldseeker.classes.Hit attribute) crossref_method (cfoldseeker.classes.Hit attribute)

D

db (cfoldseeker.classes.Hit attribute) db_id (cfoldseeker.classes.Hit attribute)

db_path (cfoldseeker.local.LocalSearch attribute) (cfoldseeker.local_clustered.LocalClusteredSearch attribute)

E

end (cfoldseeker.classes.Cluster attribute) end() (cfoldseeker.classes.Hit method) evalue (cfoldseeker.classes.Hit attribute)

expand_sequence_clusters() (cfoldseeker.local_clustered.LocalClusteredSearch method) extract_genomic_information_ena() (in module cfoldseeker.remote_parsers) extract_genomic_information_kegg() (in module cfoldseeker.remote_parsers) extract_scaffold_mapping_kegg() (in module cfoldseeker.remote_parsers)

F

fetch_taxon_names() (in module cfoldseeker.build_cds_db)

filelabel (cfoldseeker.classes.Cluster attribute)

G

generate_cblaster_session() (cfoldseeker.classes.Search method)

generate_output() (cfoldseeker.classes.Search method) generate_tables() (cfoldseeker.classes.Search method)

H

Hit (class in cfoldseeker.classes)

hits (cfoldseeker.classes.Cluster attribute) (cfoldseeker.classes.Search attribute)

I

identify_clusters() (cfoldseeker.classes.Search method) identify_clusters_from_groups() (cfoldseeker.classes.Search method) identify_hits() (cfoldseeker.classes.Search method) (cfoldseeker.local.LocalSearch method) (cfoldseeker.local_clustered.LocalClusteredSearch method) (cfoldseeker.remote.RemoteSearch method)

identify_proximal_groups() (cfoldseeker.classes.Search method) init_search() (in module cfoldseeker.main) intergenic_distance() (cfoldseeker.classes.Hit method)

L

length (cfoldseeker.classes.Cluster attribute) length() (cfoldseeker.classes.Hit method) LocalClusteredSearch (class in cfoldseeker.local_clustered)

LocalSearch (class in cfoldseeker.local) locate_nucleotide_sequences() (in module cfoldseeker.extract_sequences) locate_protein_sequences() (in module cfoldseeker.extract_sequences)

M

main() (in module cfoldseeker.build_cds_db) (in module cfoldseeker.extract_sequences) (in module cfoldseeker.main) module cfoldseeker.build_cds_db cfoldseeker.classes cfoldseeker.communication cfoldseeker.extract_sequences cfoldseeker.local cfoldseeker.local_clustered cfoldseeker.main cfoldseeker.remote cfoldseeker.remote_parsers

N

name (cfoldseeker.classes.Hit attribute)

number (cfoldseeker.classes.Cluster attribute)

O

OUTPUT_DIR (cfoldseeker.classes.Search attribute)

output_flags (cfoldseeker.classes.Search attribute)

P

params (cfoldseeker.classes.Search attribute) parse_and_validate_arguments() (in module cfoldseeker.build_cds_db) (in module cfoldseeker.extract_sequences) (in module cfoldseeker.main) parse_files() (in module cfoldseeker.build_cds_db) parse_foldseek_results() (cfoldseeker.local.LocalSearch method)

passes_criteria() (cfoldseeker.remote.RemoteSearch method) prepare_mapping_dict() (cfoldseeker.remote.RemoteSearch method) pull_and_parse_genpept_records() (cfoldseeker.remote.RemoteSearch method) pull_and_parse_kegg_records() (cfoldseeker.remote.RemoteSearch method) pull_dict_from_unisave() (in module cfoldseeker.communication) pull_from_ena() (in module cfoldseeker.communication) pull_from_unisave() (in module cfoldseeker.communication)

Q

qcov (cfoldseeker.classes.Hit attribute)

query (cfoldseeker.classes.Hit attribute) (cfoldseeker.classes.Search attribute)

R

read_genome() (in module cfoldseeker.build_cds_db) (in module cfoldseeker.extract_sequences) RemoteSearch (class in cfoldseeker.remote) retrieve_foldseek_results() (in module cfoldseeker.communication) run() (cfoldseeker.classes.Search method) (cfoldseeker.local.LocalSearch method) (cfoldseeker.local_clustered.LocalClusteredSearch method) (cfoldseeker.remote.RemoteSearch method)

run_foldseek() (cfoldseeker.classes.Search method) (cfoldseeker.local.LocalSearch method) (cfoldseeker.remote.RemoteSearch method) run_workflow() (in module cfoldseeker.build_cds_db) (in module cfoldseeker.extract_sequences) (in module cfoldseeker.main)

S

same_location() (cfoldseeker.classes.Hit method) scaff (cfoldseeker.classes.Cluster attribute) (cfoldseeker.classes.Hit attribute) score (cfoldseeker.classes.Cluster attribute) (cfoldseeker.classes.Hit attribute) Search (class in cfoldseeker.classes) select_clusters() (in module cfoldseeker.extract_sequences) seq_clust (cfoldseeker.local_clustered.LocalClusteredSearch attribute)

seqid (cfoldseeker.classes.Hit attribute) set_taxon_labels() (in module cfoldseeker.build_cds_db) setup_logging() (in module cfoldseeker.build_cds_db) (in module cfoldseeker.extract_sequences) (in module cfoldseeker.main) start (cfoldseeker.classes.Cluster attribute) start() (cfoldseeker.classes.Hit method) strand (cfoldseeker.classes.Hit attribute) submit_foldseek_query() (in module cfoldseeker.communication)

T

taxon_id (cfoldseeker.classes.Cluster attribute) (cfoldseeker.classes.Hit attribute) taxon_name (cfoldseeker.classes.Cluster attribute) (cfoldseeker.classes.Hit attribute)

tcov (cfoldseeker.classes.Hit attribute) TEMP_DIR (cfoldseeker.classes.Search attribute)

U

update_version_digits() (cfoldseeker.remote.RemoteSearch method)

W

write_cluster_genbanks() (in module cfoldseeker.extract_sequences)