taxaid API reference

class taxadb2.taxid.TaxID(**kwargs)

Main class for querying taxid

Provide methods to request taxa table and get associated accession ids.

Parameters:

**kwargs – Arbitrary arguments. Supported (username, password, port, hostname, config, dbtype, dbname)

Raises:

SystemExit – If table taxa does not exist

__init__(**kwargs)
has_parent(taxid, parent)

Check if a taxid has a parent in its lineage

Given a taxid and a parent in the form of a taxid or a scientific name,

return True if the taxid contains the parent in its lineage

Parameters:

  • taxid (int) – a taxid

  • parent (int|str) – taxid or scientific name

Returns:

True if the taxid contains the parent in its lineage, False

otherwise. None if taxid not found

Return type:

bool

lineage_id(taxid, ranks=False, reverse=False)

Get lineage for a taxonomic id

Given a taxid, return its associated lineage (in the form of a list of

taxids, each parents of each others)

Parameters:

  • taxid (int) – a taxid

  • ranks (bool) – Wether to return the the tax ranks or not. Default False

  • reverse (bool) – Inverted lineage, from top to bottom taxonomy hierarchy. Default False

Returns:

lineage_list, associated lineage id with taxid or None if

taxid not found

Return type:

list

lineage_name(taxid, ranks=False, reverse=False)

Get a lineage name for a taxonomic id

Given a taxid, return its associated lineage

Parameters:

  • taxid (int) – a taxid

  • ranks (bool) – Wether to return the tax ranks or not. Default False

  • reverse (bool) – Inverted lineage, from top to bottom taxonomy hierarchy. Default False

Returns:

lineage_name, associated lineage name with taxid or None if

taxid not found

Return type:

list

sci_name(taxid)

Get taxonomic scientific name for taxonomy id

Given a taxid, return its associated scientific name

Parameters:

taxid (int) – a taxid

Returns:

name, scientific name or None if taxid not found

Return type:

str