Constructors

`taxidTools.factories.read_taxdump(nodes, rankedlineage, merged=None, skip_synth=False, skip_env=False, skip_nodiv=True)`

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 to the merged.mp file
skip_synth (Optional[bool], default: False ) –

Skip taxa in the 'Synthetic and Chimeric' division
skip_env (Optional[bool], default: False ) –

Skip taxa in the 'Environmental samples' division
skip_nodiv (Optional[bool], default: True ) –

Skip taxa in the 'Unassigned' division

Returns:

Taxonomy –

Examples:

>>> tax = read_taxdump("nodes.dmp', 'rankedlineage.dmp')
>>> tax = read_taxdump("nodes.dmp', 'rankedlineage.dmp', merged='merged.dmp', skip_env=True, skip_synth=True)

`taxidTools.factories.read_json(path)`

Load a Taxonomy from a previously exported json file.

Parameters:

path (str) –

Path of file to load

Returns:

Taxonomy –