Index

_

__del__() (taxadb2.taxadb.TaxaDB method) __init__() (taxadb2.accessionid.AccessionID method) (taxadb2.parser.Accession2TaxidParser method) (taxadb2.parser.TaxaDumpParser method) (taxadb2.parser.TaxaParser method) (taxadb2.schema.DatabaseFactory method) (taxadb2.taxadb.TaxaDB method) (taxadb2.taxid.TaxID method)

__repr__() (taxadb2.schema.Accession method) (taxadb2.schema.DeprecatedTaxID method) (taxadb2.schema.Taxa method) __weakref__ (taxadb2.parser.TaxaParser attribute) (taxadb2.schema.DatabaseFactory attribute) (taxadb2.taxadb.TaxaDB attribute) _load_config() (taxadb2.schema.DatabaseFactory method) _set_args() (taxadb2.schema.DatabaseFactory method) _unmapped_taxid() (taxadb2.taxadb.TaxaDB method)

A

Accession (class in taxadb2.schema) accession (taxadb2.schema.Accession attribute)

accession2taxid() (taxadb2.parser.Accession2TaxidParser method) Accession2TaxidParser (class in taxadb2.parser) AccessionID (class in taxadb2.accessionid)

C

cache_merged_taxids() (taxadb2.parser.TaxaParser static method) cache_taxids() (taxadb2.parser.TaxaParser static method) check_file() (taxadb2.parser.TaxaParser static method)

check_list_ids() (taxadb2.taxadb.TaxaDB static method) check_table_exists() (taxadb2.taxadb.TaxaDB method) create_db() (in module taxadb2.app)

D

DatabaseFactory (class in taxadb2.schema) DeprecatedTaxID (class in taxadb2.schema) DoesNotExist (taxadb2.schema.Accession attribute) (taxadb2.schema.DeprecatedTaxID attribute) (taxadb2.schema.Taxa attribute)

download_files() (in module taxadb2.app)

G

get() (taxadb2.schema.DatabaseFactory method) (taxadb2.taxadb.TaxaDB method)

get_database() (taxadb2.schema.DatabaseFactory method)

H

has_parent() (taxadb2.taxid.TaxID method)

I

id (taxadb2.schema.Accession attribute)

L

lineage_id() (taxadb2.accessionid.AccessionID method) (taxadb2.taxid.TaxID method)

lineage_level (taxadb2.schema.Taxa attribute) lineage_name() (taxadb2.accessionid.AccessionID method) (taxadb2.taxid.TaxID method)

M

MAX_LIST (taxadb2.taxadb.TaxaDB attribute) md5_check() (in module taxadb2.util) module taxadb2.accessionid taxadb2.app taxadb2.parser taxadb2.schema taxadb2.taxadb taxadb2.taxid taxadb2.util

N

ncbi_taxid (taxadb2.schema.Taxa attribute)

P

parent_taxid (taxadb2.schema.Taxa attribute)

R

resolve_taxid() (taxadb2.parser.TaxaDumpParser method)

S

sci_name() (taxadb2.accessionid.AccessionID method) (taxadb2.taxid.TaxID method) set() (taxadb2.schema.DatabaseFactory method) (taxadb2.taxadb.TaxaDB method)

set_accession_file() (taxadb2.parser.Accession2TaxidParser method) set_config() (taxadb2.schema.DatabaseFactory method) set_merged_file() (taxadb2.parser.TaxaDumpParser method) set_names_file() (taxadb2.parser.TaxaDumpParser method) set_nodes_file() (taxadb2.parser.TaxaDumpParser method)

T

tax_name (taxadb2.schema.Taxa attribute) Taxa (class in taxadb2.schema) TaxaDB (class in taxadb2.taxadb) taxadb2.accessionid module taxadb2.app module taxadb2.parser module taxadb2.schema module

taxadb2.taxadb module taxadb2.taxid module taxadb2.util module TaxaDumpParser (class in taxadb2.parser) TaxaParser (class in taxadb2.parser) taxdump() (taxadb2.parser.TaxaDumpParser method) TaxID (class in taxadb2.taxid) taxid (taxadb2.schema.Accession attribute) taxid() (taxadb2.accessionid.AccessionID method)