"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()