Ancestral interactome inference

What it does

For each edge present in the interactome of at least two extant taxa

1: present / 0: absent

          -- 1 X--O (edge present in the interactome of this species)         
       --|
      |   -- 1 X--O (edge present in the interactome of this species)
    --|
   |  |   -- 0
 --|   --|
   |      -- 0 
   |
    -------- 1 X--O (edge present in the interactome of this species)

Returns the evolutionary history of the edge along the tree inferred by parsimony. This allows ancestral interactomes inference.

          -- 1 X--O
      1--|
      |   -- 1 X--O
   1--|
   |  |   -- 0
1--|  0--|
   |      -- 0
   |
    -------- 1 X--O

Installation

pip install ete3
cd <your_install_directory>
clone https://github.com/TeamAIRE/ancestral_interactome_inference.git

Usage

Run on linux, with python3

usage: ancestral_interactome_inference.py [-h] [-t TREE] [-e EDGES_DIR]
                                          [-o OUTDIR]

optional arguments:
  -h, --help    show this help message and exit
  -t TREE       path to the reference phylogenetic tree in Newick
  -e EDGES_DIR  path to directory where networks/edges are stored, each under
                the name <taxon_name_on_the_tree>__<whatever_suffix>
  -o OUTDIR     path to the output dir

Format of input data

see ancestral_interactome_inference/first_lines_of_input_data_files_to_visualize_format for examples

• TREE

A phylogenetic tree of the taxa for which interactome data is available (in newick)

• EDGES_DIR

A directory where the interactomes are stored.

Each interactome file must be named according to the corresponding taxon name (as referenced on the leaves of the aformentionned tree) followed by "__" and whatever suffix. An interactome file is a tabular file (tab-separated tsv file) with no header and two columns (nodeA, nodeB). Each line corresponds to an edge. Each node (protein) must be named according to the orthologous group id in order to allow comparisons of interactomes between extant taxa.