self.determine_variable_positions() self.estimate_frequencies(tasks = ["mutations", "clades", "tree"]) if 'genotype_frequencies' in steps: self.estimate_frequencies(tasks = ["genotypes"]) self.dump() if 'export' in steps: self.temporal_regional_statistics() # exporting to json, including the BYam specific fields self.export_to_auspice(tree_fields = ['ep', 'ne', 'rb', 'aa_muts','accession','isolate_id', 'lab','db','country'], annotations = ['2', '3', '3a']) self.generate_indexHTML() if __name__=="__main__": all_steps = ['filter', 'align', 'clean', 'tree', 'ancestral', 'refine', 'frequencies','genotype_frequencies', 'export'] from process import parser, shift_cds params = parser.parse_args() lt = time.localtime() num_date = round(lt.tm_year+(lt.tm_yday-1.0)/365.0,2) params.time_interval = (num_date-params.years_back, num_date) if params.interval is not None and len(params.interval)==2 and params.interval[0]<params.interval[1]: params.time_interval = (params.interval[0], params.interval[1]) dt= params.time_interval[1]-params.time_interval[0] params.pivots_per_year = 12.0 if dt<5 else 6.0 if dt<10 else 3.0 steps = all_steps[all_steps.index(params.start):(all_steps.index(params.stop)+1)] if params.skip is not None: for tmp_step in params.skip: if tmp_step in steps: print "skipping",tmp_step steps.remove(tmp_step)
self.generate_indexHTML()
self.export_HI_mutation_effects()
if 'HIvalidate' in steps:
print "--- generating validation figures " + time.strftime(
"%H:%M:%S") + " ---"
self.generate_validation_figures()
if __name__ == "__main__":
all_steps = [
'filter', 'align', 'clean', 'tree', 'ancestral', 'refine',
'frequencies', 'HI', 'export'
] + ['HIvalidate']
from process import parser
params = parser.parse_args()
lt = time.localtime()
num_date = round(lt.tm_year + (lt.tm_yday - 1.0) / 365.0, 2)
params.time_interval = (num_date - params.years_back, num_date)
if params.interval is not None and len(
params.interval) == 2 and params.interval[0] < params.interval[1]:
params.time_interval = (params.interval[0], params.interval[1])
dt = params.time_interval[1] - params.time_interval[0]
params.pivots_per_year = 12.0 if dt < 5 else 6.0 if dt < 10 else 3.0
steps = all_steps[all_steps.index(params.start):(
all_steps.index(params.stop) + 1)]
if params.skip is not None:
for tmp_step in params.skip:
if tmp_step in steps:
print "skipping", tmp_step
