Index

A

assigned_by (gtdblib.db.common.LpsnHtml attribute)

assigned_by_doi (gtdblib.db.common.LpsnHtml attribute)

B

basonym (gtdblib.db.common.LpsnHtml attribute) BioError

bootstrap_merge() (in module gtdblib.cli.tree) bootstrap_merge_replicates() (in module gtdblib.tree.bootstrap_merge)

C

c (gtdblib.taxonomy.taxonomy.Taxonomy attribute) canonical_gid() (in module gtdblib.util.bio.accession) category (gtdblib.db.common.LpsnHtml attribute) check_dependencies() (in module gtdblib.util.shell.execute) check_dir_exists() (in module gtdblib.util.shell.gtdbshutil) check_file_exists() (in module gtdblib.util.shell.gtdbshutil) check_on_path() (in module gtdblib.util.shell.execute) child_page_id (gtdblib.db.common.LpsnHtmlChildTaxa attribute)

CLASS (gtdblib.taxon.rank.TaxonRank attribute) CLASS_INDEX (gtdblib.taxonomy.taxonomy.Taxonomy attribute) collapse_polytomy() (in module gtdblib.tree.polytomy) collapse_polytomy_tree() (in module gtdblib.tree.polytomy) Common (class in gtdblib.db.common) convert_to_canonical() (in module gtdblib.cli.tree) convert_tree_accessions_to_canonical() (in module gtdblib.tree.convert_accession) create_label() (in module gtdblib.util.bio.newick) created (gtdblib.db.common.LpsnHtml attribute)

D

d (gtdblib.taxonomy.taxonomy.Taxonomy attribute) data (gtdblib.file.itol.collapse.iTolCollapseFile attribute) (gtdblib.file.itol.dataset_color_strip.iTolDatasetColorStripFile attribute) (gtdblib.file.itol.dataset_text.iTolDatasetTextFile attribute) (gtdblib.file.itol.label.iTolLabelFile attribute) (gtdblib.file.itol.popup.iTolPopupFile attribute) (gtdblib.file.itol.tree_colors.iTolTreeColorsFile attribute)

doi (gtdblib.db.common.LpsnHtmlNotes attribute) DOMAIN (gtdblib.taxon.rank.TaxonRank attribute) DOMAIN_INDEX (gtdblib.taxonomy.taxonomy.Taxonomy attribute) duplicate_names() (in module gtdblib.taxonomy.validation)

E

effective_publication (gtdblib.db.common.LpsnHtml attribute) effective_publication_doi (gtdblib.db.common.LpsnHtml attribute)

emendations (gtdblib.db.common.LpsnHtml attribute) etymology (gtdblib.db.common.LpsnHtml attribute) extract_seqs() (in module gtdblib.util.bio.seq_io)

F

f (gtdblib.taxonomy.taxonomy.Taxonomy attribute) FAMILY (gtdblib.taxon.rank.TaxonRank attribute)

FAMILY_INDEX (gtdblib.taxonomy.taxonomy.Taxonomy attribute) File (class in gtdblib.file) fill_trailing_ranks() (in module gtdblib.taxonomy.taxonomy)

G

g (gtdblib.taxonomy.taxonomy.Taxonomy attribute) gender (gtdblib.db.common.LpsnHtml attribute) GenericEngine (class in gtdblib.db) GENUS (gtdblib.taxon.rank.TaxonRank attribute) GENUS_INDEX (gtdblib.taxonomy.taxonomy.Taxonomy attribute) get_num_lines() (in module gtdblib.util.shell.gtdbshutil) get_tree_node_depth() (in module gtdblib.tree.get_node_depth) get_tree_node_to_desc_taxa() (in module gtdblib.tree.get_node_to_desc_taxa) get_tree_unique_mrca_for_internal_nodes() (in module gtdblib.tree.get_unique_mrca_for_internal_nodes) gtdblib module gtdblib.cli module gtdblib.cli.tree module gtdblib.config module gtdblib.db module gtdblib.db.common module gtdblib.exception module gtdblib.file module gtdblib.file.itol module gtdblib.file.itol.collapse module gtdblib.file.itol.dataset_color_strip module gtdblib.file.itol.dataset_text module gtdblib.file.itol.label module gtdblib.file.itol.popup module gtdblib.file.itol.tree_colors module gtdblib.taxon module gtdblib.taxon.rank module gtdblib.taxon.taxon module gtdblib.taxonomy module

gtdblib.taxonomy.taxonomy module gtdblib.taxonomy.validation module gtdblib.tree module gtdblib.tree.bootstrap_merge module gtdblib.tree.convert_accession module gtdblib.tree.get_node_depth module gtdblib.tree.get_node_to_desc_taxa module gtdblib.tree.get_unique_mrca_for_internal_nodes module gtdblib.tree.polytomy module gtdblib.util module gtdblib.util.bio module gtdblib.util.bio.accession module gtdblib.util.bio.exceptions module gtdblib.util.bio.newick module gtdblib.util.bio.seq_io module gtdblib.util.color module gtdblib.util.shell module gtdblib.util.shell.color module gtdblib.util.shell.execute module gtdblib.util.shell.filemgmt module gtdblib.util.shell.gtdbshutil module gtdblib.util.types module GtdbLibException GtdbLibExit

H

hex_to_rgb() (in module gtdblib.util.shell.color)

html (gtdblib.db.common.LpsnHtml attribute)

I

id (gtdblib.db.common.LpsnHtml attribute) (gtdblib.db.common.LpsnHtmlChildTaxa attribute) (gtdblib.db.common.LpsnHtmlNotes attribute) (gtdblib.db.common.LpsnHtmlSynonyms attribute) ijsem_list (gtdblib.db.common.LpsnHtml attribute) ijsem_list_doi (gtdblib.db.common.LpsnHtml attribute) InputFileError insert() (gtdblib.file.itol.collapse.iTolCollapseFile method) (gtdblib.file.itol.dataset_color_strip.iTolDatasetColorStripFile method) (gtdblib.file.itol.dataset_text.iTolDatasetTextFile method) (gtdblib.file.itol.label.iTolLabelFile method) (gtdblib.file.itol.popup.iTolPopupFile method) insert_branch() (gtdblib.file.itol.tree_colors.iTolTreeColorsFile method) insert_clade() (gtdblib.file.itol.tree_colors.iTolTreeColorsFile method)

insert_label() (gtdblib.file.itol.tree_colors.iTolTreeColorsFile method) insert_label_background() (gtdblib.file.itol.tree_colors.iTolTreeColorsFile method) insert_range() (gtdblib.file.itol.tree_colors.iTolTreeColorsFile method) is_executable() (in module gtdblib.util.shell.execute) is_float() (in module gtdblib.util.types) is_nucleotide() (in module gtdblib.util.bio.seq_io) is_protein() (in module gtdblib.util.bio.seq_io) is_same_accn_version() (in module gtdblib.util.bio.accession) iTolCollapseFile (class in gtdblib.file.itol.collapse) iTolDatasetColorStripFile (class in gtdblib.file.itol.dataset_color_strip) iTolDatasetTextFile (class in gtdblib.file.itol.dataset_text) iTolLabelFile (class in gtdblib.file.itol.label) iTolPopupFile (class in gtdblib.file.itol.popup) iTolTreeColorsFile (class in gtdblib.file.itol.tree_colors)

K

kind (gtdblib.db.common.LpsnHtmlSynonyms attribute)

L

LpsnHtml (class in gtdblib.db.common) LpsnHtmlChildTaxa (class in gtdblib.db.common)

LpsnHtmlNotes (class in gtdblib.db.common) LpsnHtmlSynonyms (class in gtdblib.db.common)

M

make_sure_path_exists() (in module gtdblib.util.shell.gtdbshutil) matching_brackets() (in module gtdblib.util.shell.filemgmt) metadata (gtdblib.db.common.Common attribute) module gtdblib gtdblib.cli gtdblib.cli.tree gtdblib.config gtdblib.db gtdblib.db.common gtdblib.exception gtdblib.file gtdblib.file.itol gtdblib.file.itol.collapse gtdblib.file.itol.dataset_color_strip gtdblib.file.itol.dataset_text gtdblib.file.itol.label gtdblib.file.itol.popup gtdblib.file.itol.tree_colors gtdblib.taxon gtdblib.taxon.rank gtdblib.taxon.taxon gtdblib.taxonomy gtdblib.taxonomy.taxonomy gtdblib.taxonomy.validation gtdblib.tree gtdblib.tree.bootstrap_merge gtdblib.tree.convert_accession gtdblib.tree.get_node_depth gtdblib.tree.get_node_to_desc_taxa gtdblib.tree.get_unique_mrca_for_internal_nodes gtdblib.tree.polytomy gtdblib.util gtdblib.util.bio gtdblib.util.bio.accession gtdblib.util.bio.exceptions gtdblib.util.bio.newick gtdblib.util.bio.seq_io gtdblib.util.color gtdblib.util.shell gtdblib.util.shell.color gtdblib.util.shell.execute gtdblib.util.shell.filemgmt gtdblib.util.shell.gtdbshutil gtdblib.util.types

N

n_child_correct (gtdblib.db.common.LpsnHtml attribute) n_child_synonym (gtdblib.db.common.LpsnHtml attribute) n_child_total (gtdblib.db.common.LpsnHtml attribute)

name (gtdblib.db.common.LpsnHtml attribute) nomenclatural_status (gtdblib.db.common.LpsnHtml attribute) (gtdblib.db.common.LpsnHtmlChildTaxa attribute) note (gtdblib.db.common.LpsnHtmlNotes attribute)

O

o (gtdblib.taxonomy.taxonomy.Taxonomy attribute) ORDER (gtdblib.taxon.rank.TaxonRank attribute)

ORDER_INDEX (gtdblib.taxonomy.taxonomy.Taxonomy attribute) original_publication (gtdblib.db.common.LpsnHtml attribute) original_publication_doi (gtdblib.db.common.LpsnHtml attribute)

P

p (gtdblib.taxonomy.taxonomy.Taxonomy attribute) page_id (gtdblib.db.common.LpsnHtmlNotes attribute) (gtdblib.db.common.LpsnHtmlSynonyms attribute) parent_page_id (gtdblib.db.common.LpsnHtmlChildTaxa attribute) parent_taxon (gtdblib.db.common.LpsnHtml attribute)

parse_label() (in module gtdblib.util.bio.newick) path (gtdblib.file.File attribute) PHYLUM (gtdblib.taxon.rank.TaxonRank attribute) PHYLUM_INDEX (gtdblib.taxonomy.taxonomy.Taxonomy attribute) polytomy() (in module gtdblib.cli.tree) proposed_as (gtdblib.db.common.LpsnHtml attribute)

R

rank (gtdblib.taxon.taxon.Taxon attribute) RANK_INDEX (gtdblib.taxonomy.taxonomy.Taxonomy attribute) RANK_LABELS (gtdblib.taxonomy.taxonomy.Taxonomy attribute) RANK_PREFIXES (gtdblib.taxonomy.taxonomy.Taxonomy attribute) read() (in module gtdblib.util.bio.seq_io) read_fasta() (in module gtdblib.util.bio.seq_io) read_fasta_seq() (in module gtdblib.util.bio.seq_io) read_fastq() (in module gtdblib.util.bio.seq_io) read_fastq_seq() (in module gtdblib.util.bio.seq_io)

read_seq() (in module gtdblib.util.bio.seq_io) read_taxonomy() (in module gtdblib.taxonomy.taxonomy) read_taxonomy_from_tree() (in module gtdblib.taxonomy.taxonomy) record_number (gtdblib.db.common.LpsnHtml attribute) registry (gtdblib.db.common.Common attribute) rgb_to_hex() (in module gtdblib.util.color) (in module gtdblib.util.shell.color) risk_group (gtdblib.db.common.LpsnHtml attribute) run() (in module gtdblib.util.shell.execute) run_bash() (in module gtdblib.util.shell.execute)

S

s (gtdblib.taxonomy.taxonomy.Taxonomy attribute) select_delimiter() (in module gtdblib.util.shell.filemgmt) seq_lengths() (in module gtdblib.util.bio.seq_io) sha256() (in module gtdblib.util.shell.filemgmt) sha256_rb() (in module gtdblib.util.shell.filemgmt) SPECIES (gtdblib.taxon.rank.TaxonRank attribute) SPECIES_INDEX (gtdblib.taxonomy.taxonomy.Taxonomy attribute)

ssu (gtdblib.db.common.LpsnHtml attribute) ssu_ebi (gtdblib.db.common.LpsnHtml attribute) ssu_fasta (gtdblib.db.common.LpsnHtml attribute) ssu_ggdc (gtdblib.db.common.LpsnHtml attribute) ssu_ncbi (gtdblib.db.common.LpsnHtml attribute) strain_info (gtdblib.db.common.LpsnHtml attribute) symlink() (in module gtdblib.util.shell.gtdbshutil) synonym_id (gtdblib.db.common.LpsnHtmlSynonyms attribute)

T

Taxon (class in gtdblib.taxon.taxon) taxonomic_consistency() (in module gtdblib.taxonomy.validation) taxonomic_status (gtdblib.db.common.LpsnHtml attribute) (gtdblib.db.common.LpsnHtmlChildTaxa attribute) Taxonomy (class in gtdblib.taxonomy.taxonomy) TaxonRank (class in gtdblib.taxon.rank) to_process (gtdblib.db.common.LpsnHtml attribute)

tygs (gtdblib.db.common.LpsnHtml attribute) type_annotation_map (gtdblib.db.common.Common attribute) type_class (gtdblib.db.common.LpsnHtml attribute) type_genus (gtdblib.db.common.LpsnHtml attribute) type_order (gtdblib.db.common.LpsnHtml attribute) type_species (gtdblib.db.common.LpsnHtml attribute) type_strain (gtdblib.db.common.LpsnHtml attribute) type_subgenus (gtdblib.db.common.LpsnHtml attribute)

U

updated (gtdblib.db.common.LpsnHtml attribute)

url (gtdblib.db.common.LpsnHtml attribute) (gtdblib.db.GenericEngine property)

V

valid_publication (gtdblib.db.common.LpsnHtml attribute) valid_publication_doi (gtdblib.db.common.LpsnHtml attribute)

validate_species_name() (in module gtdblib.taxonomy.validation) validate_taxonomy() (in module gtdblib.taxonomy.validation) value (gtdblib.taxon.taxon.Taxon attribute)

W

which() (in module gtdblib.util.shell.execute) write() (gtdblib.file.itol.collapse.iTolCollapseFile method) (gtdblib.file.itol.dataset_color_strip.iTolDatasetColorStripFile method) (gtdblib.file.itol.dataset_text.iTolDatasetTextFile method) (gtdblib.file.itol.label.iTolLabelFile method) (gtdblib.file.itol.popup.iTolPopupFile method) (gtdblib.file.itol.tree_colors.iTolTreeColorsFile method)

write_fasta() (in module gtdblib.util.bio.seq_io)