Add draft parser for mykrobe

[pvanheus]

This adds a parser for results from mykrobe. This parser is still incomplete:

1. nucleotide_change cannot be computed from the mykrobe results
2. drug_class does not use ARO terms
3. computation of frequency and depth of coverage needs to be checked with mykrobe tool authors

[iqbal-lab]

Comments from me (one of the mykrobe folk)

1. Nucleotide change indeed cannot be inferred from the mykrobe results, though in future we could look into making that visible.
2. what are ARO terms?
3. The json output contains a number of tags: percent_coverage refers to proportion of the probe that has coverage - there is a probe for an allele. ideally this should be 100. median_depth is the depth of coverage on the allele.

does this help?

[fmaguire]

1. Would making an issue on the mykrobe repo be useful as a possible future extension?
2. ARO is the antibiotic resistance ontology that CARD and a few other resources are built on top of (or map back to). A nice helper for standardisation across the myriad of AMR databases and tools!
3. Thanks, that's really useful!