The main part of Deciphon is its core. It is implemented in C and built on top of IMM library to define protein using hidden Markov models and perform inference using the Viterbi method.
Its command-line interface can be installed by
pip install deciphonif you have a working Python environment. It will run on MacOS and Linux operating systems. After installing it, just enter
deciphon --helpin the terminal to show usage information.
├─ c-core/ Deciphon library written in C.
├─ cli/ Command-line interface written in Python.
├─ control/ Command-line interface to control and run the servers.
├─ eval/ Python scripts to evaluate its performance.
├─ python-core/ Python wrapper around the Deciphon library.
├─ sched/ RESTful API for Deciphon server in Python.
├─ snap/ Reader for Deciphon snap files written in Python.
├─ tests/ Unit tests.
The relevant files are compose.yml and compose.cfg. You can launch it via docker compose --env-file compose.cfg up and test it running ./tests/test-compose.sh. Once it is running, open http://127.0.0.1:1515/docs to have an overview of the RESTful API.
You might want to change the variable DECIPHON_SCHED_ALLOW_ORIGINS in the file compose.cfg to the hostname of a web server.
Give a ⭐️ if this project helped you!