"threshold": params.viruses_per_month,
"category": lambda x:(x.attributes['date'].year, x.attributes['date'].month, x.attributes['country'])
},
"colors": ["authors", "country", "region"],
"color_defs": ["./colors.tsv"],
"lat_longs": ["country", "region"],
"auspice_filters": ["authors", "region", "country"],
"reference": {
"path": "measles-reference.gb",
"metadata": {
'strain': "Ichinose-B95a", "accession": "NC_001498.1", "date": "XXXX-XX-XX",
'host': "human", 'country': "Unknown", 'region': "Unknown"
},
"include": 0,
"genes": ['N', 'P', 'V', 'C', 'M', 'F', 'H', 'L']
}
}
return config
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()
}
return config
if __name__=="__main__":
parser = collect_args()
params = parser.parse_args()
if 'multiple' in params.serotypes:
params.serotypes = ['denv1', 'denv2', 'denv3', 'denv4', 'all']
# else:
# params.serotypes = params.serotypes]
# modify config file according to serotype
for serotype in params.serotypes:
print("Preparing serotype %s"%serotype)
config = make_config(serotype, params)
if params.viruses_per_month == 0:
config["subsample"] = False
else:
config["subsample"]["threshold"] = params.viruses_per_month
runner = prepare(config)
runner.load_references()
runner.applyFilters()
runner.subsample()
runner.colors()
runner.latlongs()
runner.write_to_json()
"sources": sources
}
return config
if __name__=="__main__":
parser = collect_args()
params = parser.parse_args()
if 'multiple' in params.serotypes:
params.serotypes = ['denv1', 'denv2', 'denv3', 'denv4', 'all']
# modify config file according to serotype
for serotype in params.serotypes:
print("Preparing serotype %s"%serotype)
config = make_config(serotype, params)
if params.viruses_per_month == 0:
config["subsample"] = False
else:
config["subsample"]["threshold"] = params.viruses_per_month
runner = prepare(config)
runner.load_references()
runner.applyFilters()
runner.subsample()
runner.colors()
runner.latlongs()
runner.write_to_json()