gtdblib package

Subpackages

• gtdblib.cli package
  • Submodules
  • gtdblib.cli.tree module
    • bootstrap_merge()
    • convert_to_canonical()
    • polytomy()
  • Module contents
• gtdblib.db package
  • Submodules
  • gtdblib.db.common module
    • Common
      • Common.metadata
      • Common.registry
      • Common.type_annotation_map
    • LpsnHtml
      • LpsnHtml.assigned_by
      • LpsnHtml.assigned_by_doi
      • LpsnHtml.basonym
      • LpsnHtml.category
      • LpsnHtml.created
      • LpsnHtml.effective_publication
      • LpsnHtml.effective_publication_doi
      • LpsnHtml.emendations
      • LpsnHtml.etymology
      • LpsnHtml.gender
      • LpsnHtml.html
      • LpsnHtml.id
      • LpsnHtml.ijsem_list
      • LpsnHtml.ijsem_list_doi
      • LpsnHtml.n_child_correct
      • LpsnHtml.n_child_synonym
      • LpsnHtml.n_child_total
      • LpsnHtml.name
      • LpsnHtml.nomenclatural_status
      • LpsnHtml.original_publication
      • LpsnHtml.original_publication_doi
      • LpsnHtml.parent_taxon
      • LpsnHtml.proposed_as
      • LpsnHtml.record_number
      • LpsnHtml.risk_group
      • LpsnHtml.ssu
      • LpsnHtml.ssu_ebi
      • LpsnHtml.ssu_fasta
      • LpsnHtml.ssu_ggdc
      • LpsnHtml.ssu_ncbi
      • LpsnHtml.strain_info
      • LpsnHtml.taxonomic_status
      • LpsnHtml.to_process
      • LpsnHtml.tygs
      • LpsnHtml.type_class
      • LpsnHtml.type_genus
      • LpsnHtml.type_order
      • LpsnHtml.type_species
      • LpsnHtml.type_strain
      • LpsnHtml.type_subgenus
      • LpsnHtml.updated
      • LpsnHtml.url
      • LpsnHtml.valid_publication
      • LpsnHtml.valid_publication_doi
    • LpsnHtmlChildTaxa
      • LpsnHtmlChildTaxa.child_page_id
      • LpsnHtmlChildTaxa.id
      • LpsnHtmlChildTaxa.nomenclatural_status
      • LpsnHtmlChildTaxa.parent_page_id
      • LpsnHtmlChildTaxa.taxonomic_status
    • LpsnHtmlNotes
      • LpsnHtmlNotes.doi
      • LpsnHtmlNotes.id
      • LpsnHtmlNotes.note
      • LpsnHtmlNotes.page_id
    • LpsnHtmlSynonyms
      • LpsnHtmlSynonyms.id
      • LpsnHtmlSynonyms.kind
      • LpsnHtmlSynonyms.page_id
      • LpsnHtmlSynonyms.synonym_id
  • Module contents
    • GenericEngine
      • GenericEngine.url
• gtdblib.exception package
  • Module contents
    • GtdbLibException
    • GtdbLibExit
• gtdblib.file package
  • Subpackages
    • gtdblib.file.itol package
      • Submodules
      • 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
      • Module contents
  • Module contents
    • File
      • File.path
• gtdblib.taxon package
  • Submodules
  • gtdblib.taxon.rank module
    • TaxonRank
      • TaxonRank.CLASS
      • TaxonRank.DOMAIN
      • TaxonRank.FAMILY
      • TaxonRank.GENUS
      • TaxonRank.ORDER
      • TaxonRank.PHYLUM
      • TaxonRank.SPECIES
  • gtdblib.taxon.taxon module
    • Taxon
      • Taxon.rank
      • Taxon.value
  • Module contents
• gtdblib.taxonomy package
  • Submodules
  • gtdblib.taxonomy.taxonomy module
    • Taxonomy
      • Taxonomy.CLASS_INDEX
      • Taxonomy.DOMAIN_INDEX
      • Taxonomy.FAMILY_INDEX
      • Taxonomy.GENUS_INDEX
      • Taxonomy.ORDER_INDEX
      • Taxonomy.PHYLUM_INDEX
      • Taxonomy.RANK_INDEX
      • Taxonomy.RANK_LABELS
      • Taxonomy.RANK_PREFIXES
      • Taxonomy.SPECIES_INDEX
      • Taxonomy.c
      • Taxonomy.d
      • Taxonomy.f
      • Taxonomy.g
      • Taxonomy.o
      • Taxonomy.p
      • Taxonomy.s
    • fill_trailing_ranks()
    • read_taxonomy()
    • read_taxonomy_from_tree()
  • gtdblib.taxonomy.validation module
    • duplicate_names()
    • taxonomic_consistency()
    • validate_species_name()
    • validate_taxonomy()
  • Module contents
• gtdblib.tree package
  • Submodules
  • gtdblib.tree.bootstrap_merge module
    • bootstrap_merge_replicates()
  • gtdblib.tree.convert_accession module
    • convert_tree_accessions_to_canonical()
  • gtdblib.tree.get_node_depth module
    • get_tree_node_depth()
  • gtdblib.tree.get_node_to_desc_taxa module
    • get_tree_node_to_desc_taxa()
  • gtdblib.tree.get_unique_mrca_for_internal_nodes module
    • get_tree_unique_mrca_for_internal_nodes()
  • gtdblib.tree.polytomy module
    • collapse_polytomy()
    • collapse_polytomy_tree()
  • Module contents
• gtdblib.util package
  • Subpackages
    • gtdblib.util.bio package
      • Submodules
      • gtdblib.util.bio.accession module
      • gtdblib.util.bio.exceptions module
      • gtdblib.util.bio.newick module
      • gtdblib.util.bio.seq_io module
      • Module contents
    • gtdblib.util.shell package
      • Submodules
      • gtdblib.util.shell.color module
      • gtdblib.util.shell.execute module
      • gtdblib.util.shell.filemgmt module
      • gtdblib.util.shell.gtdbshutil module
      • Module contents
  • Submodules
  • gtdblib.util.color module
    • rgb_to_hex()
  • gtdblib.util.types module
    • is_float()
  • Module contents

Submodules

gtdblib.config module

Module contents