Constructors

taxidTools.factories.read_taxdump(nodes, rankedlineage, merged=None)

Read a Taxonomy from the NCBI`s taxdump files

Parameters:

• nodes (str) –

  Path to the nodes.dmp file

• rankedlineage (str) –

  Path to the rankedlineage.dmp file

• merged (Optional[str], default: None ) –

  Path tothe merged.mp file

Returns:

• Taxonomy –

Examples:

>>> tax = read_taxdump("nodes.dmp', 'rankedlineage.dmp')

See Also

read_json

taxidTools.factories.read_json(path)

Load a Taxonomy from a previously exported json file.

Parameters:

• path (str) –

  Path of file to load

Returns:

• Taxonomy –

See Also

taxidTools.Taxonomy.write read_taxdump