IgMAT is a tool for the automatic discrimination and annotation of antibody sequences, specifically designed to be integrated into analysis pipelines or being used as a cli tool. IgMAT is highly customizable, allowing the addition of custom antibody sequences datasets and generating a range of output formats including a bed file of FR and CDR coordinates allowing simple downstream analysis on individual regions.
- Python version 3.8 or greater
- Hmmer
IgMAT can be installed locally or in a python environment:
git clone git@github.com:TPI-Immunogenetics/igmat.git
cd igmat
python3 -m venv env
source env/bin/activate
pip install ./
The default HMM model generated from IMGT data needs to be build in order to run IgMAT:
igmat build
Once done, to exit the environment, type:
deactivate
IgMAT will automatically generate a configuration file in the user home directory:
~/.igmat/config.yaml
All generated hmmer models will be stored in this folder and the configuration file will be automatically initialised with the path containing the hmmer executables. For each one of the cli tools, the option --hmmerpath is available to temporarily override the hmmer path.
IgMAT comes with a set of cli tools for handling custom HMM models and processing data:
igmat <tool> --help
Where tool is one of the following:
- run: process the input sequence/file and run the annotation script.
- build: build custom HMM models
- list: handles the available HMM models
IgMAT can be used as a stand alone tool, or embedded into a custom script. Please check the examples and a tutorial about embedding IgMAT in your scripts.