Python API for the Interactive Tree of Life (iTOL)
Created by Albert Wang (albertyw at mit.edu)
With Complements to: iTOL (Interactive Tree of Life), Python requests package.
This iTOL API allows local software to upload trees to iTOL using Itol.py
and export uploaded trees using ItolExport.py using direct Python
calls or through shell. An active internet connection to the
iTOL website is required.
pip install itolapi
(If you need to do anything more than displaying basic tree structures, you must call the Python iTOL API from within a Python program)
$ Itol.py /path/to/example.tree http://itol.embl.de/external.cgi?tree=1234567890&restore_saved=1
Running from a python program is much more flexible than running from command line and allows access to all iTOL options
from itolapi import Itol
itol_uploader = Itol.Itol()
itol_uploader.add_variable('treeFile', '/path/to/example.tree')
itol_uploader.add_variable('treeFormat', 'newick')
itol_uploader.add_variable('treeName', 'apple')
status = itol_uploader.upload()
assert status != False
itol_uploader.comm.upload_output
# SUCCESS: 1234567890
itol_uploader.comm.tree_id
# 1234567890
itol_uploader.get_webpage()
# http://itol.embl.de/external.cgi?tree=1234567890&restore_saved=1
itol_uploader.get_itol_export()
# <ItolExport.ItolExport instance at 0x207c5f0>
An example for using the Python iTOL API can found in
examples/example.py.
(If you would like to set any parameters other than the tree id, location to save the file, file format, and whether to display datasets, you must use ItolExport from a Python program)
$ ItolExport.py TREEID FILELOCATION FORMAT [OPTIONS]
- Options include:
-d: show datasets-r: verbose output-h: help
Running ItolExport.py from a Python program allows you to use all the options that iTOL has available.
from itolapi import ItolExport
itol_exporter = ItolExport.ItolExport()
itol_exporter.add_export_param_value('tree', tree_id)
assert format in ['png', 'svg', 'eps', 'ps', 'pdf', 'nexus', 'newick']
itol_exporter.add_export_param_value('format', format)
itol_exporter.add_export_param_value(param_key, param_value)
itol_exporter.export(file_location)
Valid param_key and param_value values can be found on the iTOL API page.
Send bugs and comments as issues on the Github repository.
To run tests:
pip install tox python setup.py install tox
To update PyPI:
python setup.py sdist upload