"subsample": {
"category": lambda x:(x.attributes['region'], x.attributes['date'].year, x.attributes['date'].month),
"threshold": params.viruses_per_month,
"priority": lambda x:x.id in forced_strains
},
"colors": ["country", "division"], # essential. Maybe False.
"color_defs": ["./colors.tsv"],
"lat_longs": ["country", "division"], # essential. Maybe False.
"reference": {
"path": "metadata/ebola_outgroup.gb",
"metadata": {
'strain': "reference", "accession": "KR075003", "date": "2014-XX-XX",
'host': "human", 'country': "Liberia"
},
"include": 0,
"genes": ['NP', 'VP35', 'VP40', 'GP', 'sGP', 'VP30', 'VP24', 'L']
}
}
if __name__=="__main__":
params = collect_args()
runner = prepare(make_config(params))
runner.load_references()
runner.applyFilters()
runner.ensure_all_segments()
runner.subsample()
runner.colors()
runner.latlongs()
runner.write_to_json()
'../../fauna/source-data/geo_lat_long.tsv',
"references":
{seg: reference_maps[lineage][seg]
for seg in params.segments},
"regions":
regions,
"time_interval":
time_interval,
}
if __name__ == "__main__":
params = collect_args()
# set_trace()
## lots of loops to allow multiple downstream analysis
for lineage in params.lineages:
for resolution in params.resolutions:
pprint("Preparing lineage {}, segments: {}, resolution: {}".format(
lineage, params.segments, resolution))
config = make_config(lineage, resolution, params)
runner = prepare(config)
runner.load_references()
runner.applyFilters()
runner.ensure_all_segments()
runner.subsample()
runner.colors()
runner.latlongs()
runner.write_to_json()
},
"include": 0,
"genes": ['NC', 'P', 'V', 'I', 'M', 'F', 'SH', 'HN', 'L']
}
}
if context == "global":
config["filters"] = (filters["dropped_strains"], filters["exclude_BC"], filters["exclude_Mass"], filters["unknown_country"])
elif context == "bc":
config["filters"] = (filters["dropped_strains"], filters["canada_only"], filters["unknown_country"])
elif context == "mass":
config["filters"] = (filters["dropped_strains"], filters["Mass_only"],filters["unknown_country"])
else:
print("Unknown context. FATAL")
sys.exit(2)
return config
if __name__=="__main__":
params = collect_args()
for context in ["global", "bc", "mass"]:
runner = prepare(make_config(context))
runner.load_references()
runner.applyFilters()
runner.ensure_all_segments()
runner.subsample()
runner.colors()
runner.latlongs()
runner.write_to_json()