itol-config
To annotate trees in iTOL requres special config files that are time-consuming to create. This python package contains functions to create configuration files automatically from a CSV file.
Installation
CLI Usage
This command will automatically create a config file for each column in the specified input csv file.
itol-config --input <input.csv> --out <prefix_for_output_files> --id <id_column> --type <annotation_type>
If you you already have colours in mind, you can specify them with the --colour-conf option. This requires a toml file with the following format:
[Column_name_1]
value1 = "colour"
value2 = "colour"
[Column_name_2]
value1 = "colour"
value2 = "colour"
Use functions in your own scripts
You can also call the functions in your own code. For example:
from itol_config import get_config_writer
import random
# generate some example data
countries = ["UK", "USA", "France", "Germany", "Spain"]
data = {f'sample_{i}': random.choice(countries) for i in range(10)}
# create a config writer
writer = get_config_writer(
config_type="colour_strip",
data=data,
label="Countries"
)
outfile = "countries_strip_config.txt"
writer.write(outfile)
Developers
The following annotation types are currently supported:
If you want to contribute a new annotation type this package, please clone the repository and create a new branch for your changes. Then create a pull request to merge your changes into the master branch.
Adding a new annotation type
Each annotation type is defined as a class in itol_config/interfaces. The class must inherit from the ConfigWriter class and implement the write method. Have a look at the existing classes for examples. Make sure to add your new class to interfaces_types dictionary in the __init__.py file in the same directory.