Group project to identify potential regulators of NMII and Fog pathway members in a fly interactome.
- Anna Ritz, professor
- Miriam Bern, student
- Wyatt Gormley, student
- Elaine Kushkowski, student
- ** Kathy Thompson**, student
- Logan Tibbetts, student
The group_proj_331.py script will generate a list of potential regulators from a protein-protein interactome and a file of positive regulator containing interactions between nodes using pre-processing techniques, Steiner Tree Approximations, Dijkstra-ranking, and a shortest paths algorithm.
- Input: a plain text file, formatted into at least 2 columns to indicate node to node interaction, a text file of regulators.
- Output: text file of the edge list of the Steiner Tree and a file containing all nodes within it, text files of potential regulators ranked by the Dijkstra-ranking, and text files of potential regulators calculated by the shortest-paths algorithm.
- Output note: "tree_nodes.txt" and "tree_edges.txt" may be different with each run because we are using a Steiner tree approximation.
- Runtime note: This code takes at least 3 hours to run on the original interactome.
Make sure that all files to be analyzed are in the same file folder as group_proj_331.py. When running, change the interactome variable in the main() function to be whatever text file interactome you are analyzing, and change the positives variable in the main() function to be a text file of positive regulators for that genome.
The purpose of post_processing.py is to produce output files from input obtained from the main file. It was also used for testing output functions separately from the main code.