accessionid API reference

class taxadb2.accessionid.AccessionID(**kwargs)

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)

lineage_id(acc_number_list)

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)

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)

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)

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)