accessionid API reference

class taxadb.accessionid.AccessionID(**kwargs)[source]

Main accession class

Provide methods to request accession table and get associated taxonomy for
accession ids.
Parameters:**kwargs – Arbitrary arguments. Supported (username, password, port, hostname, config, dbtype, dbname)
Raises:SystemExit – If table accession does not exist
__init__(**kwargs)[source]

Initialize self. See help(type(self)) for accurate signature.

lineage_id(acc_number_list)[source]

Get taxonomic lineage name for accession ids

Given a list of accession numbers, yield the accession number and their
associated lineage (in the form of taxids) as tuples
Parameters:acc_number_list (list) – a list of accession numbers
Yields:tuple – (accession id, lineage list)
lineage_name(acc_number_list)[source]

Get a lineage name for accession ids

Given a list of acession numbers, yield the accession number and their
associated lineage as tuples
Parameters:acc_number_list (list) – a list of accession numbers
Yields:tuple – (accession id, lineage name)
sci_name(acc_number_list)[source]

Get taxonomic scientific name for accession ids

Given a list of accession numbers, yield the accession number and their associated scientific name as tuples

Parameters:acc_number_list (list) – a list of accession numbers
Yields:tuple – (accession id, taxonomy id)
taxid(acc_number_list)[source]

Get taxonomy of accession ids

Given a list of accession numbers, yield the accession number and their associated taxids as tuples

Parameters:acc_number_list (list) – a list of accession numbers
Yields:tuple – (accession id, taxonomy id)