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README.md

iTOL Python API

PyPI PyPI - Python Version PyPI - License

Codeship Status for albertyw/itolapi codecov Maintainability Updates

Notice: Due to iTOL requiring paid subscriptions for batch uploads, this library will be deprecated after October 1, 2020.

Python API for the Interactive Tree of Life (iTOL)

Created by Albert Wang (git at albertyw.com)

With Complements to iTOL (Interactive Tree of Life).

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.

Installation

pip install itolapi

Uploading Trees To iTOL (itol.py)

From Command Line

(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

From Python

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_uploader.add_file('/path/to/example.tree')
itol_uploader.params['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.

Downloading Trees From iTOL (itolexport.py)

From Command Line

(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
  • -v: verbose output
  • -h: help

From Python

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()
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.

Bugs/Comments

Send bugs and comments as issues on the itolapi Github repository.

Development

To run tests:

python setup.py install
pip install -r requirements-test.txt
mypy itolapi
coverage run setup.py
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