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:
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Genome block information files.
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A csv file mapping accession numbers to corresponding organism names.
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A newick formatted phylogenetic tree.
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An event pickled dictionary containing each operon's events and number of their observations.
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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:
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CSV files with all the z-scores in each operon's event
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Directory with genome diagrams alone.
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Directory with diagram containing tree, genome diragram and heat map for each operon event.