4. Scripts and API documentation

4.1. Scripts

About the pipeline:

  1. make_pairs.py which computes the contacts of pairs of genes.
  2. join_pairs.py which extracts the intersection of pairs from two tables of contacts. The intersection is computed using the orthologs.
  3. From there, we have two possibilities:

Tools (not exhaustive):

  • statshic.py computes basic statistics over a dataset and output the results directly or write it as JSON.
  • norm_center.py normalizes a buch of dataset in order to make them comparable with each other.
  • informative_traits.py reports information about the traits that are informative, i.e. the traits that don’t have the same value in all species.

Scripts usage:

4.2. API

The scripts make use of the following modules: