operonVisualization

Evolution of gene blocks in proteobacteria can be described by a small set of events: insertions, deletions and duplications. The figures generated will help understand the evolutionary rate.

This program requires the following inputs:

1. Genome block information files.

2. A csv file mapping accession numbers to corresponding organism names.

3. A newick formatted phylogenetic tree.

4. An event pickled dictionary containing each operon's events and number of their observations.

5. An output directory of user's choice.

Note: Samples for each of the inputs are available in 'data' folder.

This command should run generate the required figures:

./operonVisual.py -n data/optimized_results_proteobacteria -m data/mapping.csv -t data/reorder.nwk -e data/event_dict.p -o [path to your choice of output directory]

Output:

1. CSV files with all the z-scores in each operon's event

2. Directory with genome diagrams alone.

3. Directory with diagram containing tree, genome diragram and heat map for each operon event.