Revised version, with
- example Python code for annotating AMRFinderPlus gene reports (parse_amrfinder.py)
- example files to test on (/example_data_kleb/ containing example AMRFinderPlus results on 5 Kleb pneumo genomes)
- example dictionary to facilitate testing, note this is a temporary fix for use in code dev/testing until CARD drug-level dictionary is available, it contains only those genes in refgenes (DB used by AMRFinderPlus) that are relevant to reporting in Klebsiella
- updated figures to reflect minor changes and real example with Kleb pneumo ERR257656