v1.1

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

v1.0

Initial proposal following Holt lab retreat, 6 June 2023