iTAK v2

iTAK identifies and classifies plant transcription factors (TFs), transcriptional regulators (TRs), and protein kinases (PKs) from genome or transcriptome sequence data.

Recommended: pixi

This is the simplest way to run iTAK from this repository because pixi manages both Python dependencies and HMMER.

1. Install dependencies

pixi install

2. Download the database

pixi run itak -- db download

3. Run iTAK

pixi run itak -- <sequence_file>

Example:

pixi run itak -- test_seq

Alternative: local pip install

Use this only if you do not want to use pixi.

Requirements:

• Python 3.8+
• hmmscan from HMMER available on PATH

Install:

python -m pip install -e .

Download the database:

itak db download

Run:

itak <sequence_file>

Conda / Bioconda

Planned, but not available yet.

The Bioconda recipe has been prepared, but it has not been accepted upstream yet. Do not use the commands below until the Bioconda package is actually published.

Planned install command:

conda install -c bioconda itak

Planned usage:

itak db download
itak <sequence_file>

Database Location

Inspect the current database location:

itak db path

Inspect the default install target:

itak db path --target

Use a custom database location:

itak db download --path /path/to/itak-db
ITAK_DB_DIR=/path/to/itak-db itak <sequence_file>

Verify database files:

itak db verify

Default lookup/install behavior:

• ITAK_DB_DIR if set
• ./database only when it already contains a valid iTAK database
• CONDA_PREFIX/share/itak/database for pixi/conda-style environments
• ~/.local/share/itak/database for user installs

Validation

pixi run validate

Documentation

More details are available in the wiki.