Protein Sequence Observation Tool

A tool that executes several bioinformatic tools for a set of protein sequences. The results of all tools are converted into json documents, enabling for simple post processing.

Supported bioinformatic tools:

• hmmer
• blastp
• signalp
• ghostx
• targetp

Getting started for development (Setup)

Prerequisites:

• git
• python3
• nextflow

Install nextflow:

curl -fsSL get.nextflow.io | bash

Checkout the repository:

git clone git@git.computational.bio.uni-giessen.de:SOaAS/psot.git

Setup a virtualenv for development and install it in editable mode:

# install in development environment
virtualenv --python=python3 venv; source venv/bin/activate;
pip install -e .

# run tests
python3 setup.py test

# compile documentation
python3 setup.py build_sphinx

At the moment the required dbxref module is not available via a public pip repository. You have to check it out via git and install it to the same virtual environment.

Use the application:

psot analyze -f example/proteins.fas -o results -p fast

Run the tests:

# all tests
python3 setup.py test

# single tests module, e.g. test_repository
python3 setup.py test -s tests.test_repository