Itol helper

A tool that simplifies uploading data to Itol and generating commonly used datasets.

Install

Since poetry is used as the package manager, run pip install poetry if necessary.

poetry install

Run

Upload

Upload a directory containing a phylogenetic tree and Itol style files. Make sure the directory does not contain anything other than the tree and style files.

usage: ih upload [-h] [--api-key API_KEY] -p PROJECT_NAME [--tree-name TREE_NAME] [--tree-description TREE_DESCRIPTION] -d DIR

options:
  -h, --help            show this help message and exit
  --api-key API_KEY     Using ITOL_APIKEY environment variable for default
  -p PROJECT_NAME, --project-name PROJECT_NAME
  --tree-name TREE_NAME
  --tree-description TREE_DESCRIPTION
  -d DIR, --dir DIR

Example

poetry run ih upload -d /path/to/upload_dir --api-key $your_api_key --project-name $your_project_name

text

Add aliases to Labels based on a config file.

usage: ih text [-h] -i IDS -c CONFIG [-l LABEL]

options:
  -h, --help            show this help message and exit
  -i IDS, --ids IDS     file contained ID (nwk, fasta, phy or txt)
  -c CONFIG, --config CONFIG
                        config file
  -l LABEL, --label LABEL

style

Change the color of Labels based on a config file.

usage: ih style [-h] -i IDS -c CONFIG [-l LABEL]

options:
  -h, --help            show this help message and exit
  -i IDS, --ids IDS     file contained ID (nwk, fasta, phy or txt)
  -c CONFIG, --config CONFIG
                        config file
  -l LABEL, --label LABEL

branch-symbols

Generate branch symbols based on a config file.

usage: ih branch-symbols [-h] -i IDS -c CONFIG [-l LABEL]

options:
  -h, --help            show this help message and exit
  -i IDS, --ids IDS     file contained ID (nwk, fasta, phy or txt)
  -c CONFIG, --config CONFIG
                        config file
  -l LABEL, --label LABEL

alignment

Convert fasta or phy format to itol alignment style.

usage: ih alignment [-h] -i INPUT [-l LABEL]

options:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        file contained multple alignment. fasta and phy are supported
  -l LABEL, --label LABEL

Config

A JSON-formatted file required to generate Itol style files.

Colormap

Specify an object with regular expressions as Keys and color codes as Values in the colormap field. This corresponds to the colors of Labels and branch-symbols.

Id to Name

Specify an object with node values as Keys and the desired display names as Values in the id_to_name field. This is used when creating aliases.

Example

{
  "colormap": {
    "^Mp": "#4b0082",
    "^Pp": "#32cd32",
    "^Apun": "#800000",
    "^Smoe": "#00bfff",
    "^Azfi|^Sacu": "#2f4f4f",
    "^MA": "#66cdaa",
    "^Nycol|^evm": "#adff2f",
    "^LOC": "#ffb6c1",
    "^AT": "#daa520",
    "^jgi": "#696969",
    "^Cre|^Ol": "#000000"
  },
  "id_to_name": {
    "AT1G29160.1": "AtCOG1",
    "AT1G26790.1": "AtCDF6",
    "AT1G69570.1": "AtCDF5",
    "AT2G46590.1": "AtDAG2",
    "AT2G34140.1": "AtCDF4",
    "AT3G47500.1": "AtCDF3",
    "AT5G39660.1": "AtCDF2",
    "AT5G62430.1": "AtCDF1"
  }
}