Typically proteomic search engines produce a single number used to rank each peptide-spectrum-match. The purpose of this tool is to allow re-evaluation of these matches using any number of flexiable criteria chosen by the user in a search engine independent manner.

The goal to reduce a large number of PSMs to a smaller number of PSMs the researcher is more confident about, perhaps as a precursor to manual visual validation or additional experimentation.

The python dependencies for PSM Evaluator are listed in requiements.txt.

1. Install virtualenv:

    pip install virtualenv
   

2. Create a new Python environment:

    virtualenv -q --no-site-packages .venv
   

3. Activate environment:

    . .venv/bin/activate
   

4. Install required dependencies into this virtual environment:

    pip install -r requirements.txt
   

For this to work you may have to install some native packages such as libxml2-dev and libyaml-dev.

You will likely want to use [these instructions][install_pyteomics] to install Pyteomics and its dependencies and then download and install the pyyaml library.

Using settings_example.yaml as an example build a settings file (lets call it settings.yaml). Then execute the main driver program as follows:

python psme/main.py --settings settings.yaml

Fork this project on github. Modify and run tests.:

pip install nosetests  # only need to do this first time.
nosetests