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) # modify clade designations if not params.ATG: virus_config, epitope_mask, receptor_binding_sites = shift_cds(3*sp, virus_config, epitope_mask, receptor_binding_sites) # add all arguments to virus_config (possibly overriding) virus_config.update(params.__dict__) # pass all these arguments to the processor: will be passed down as kwargs through all classes myBYam = BYam_process(**virus_config) if params.test: myBYam.load() else: myBYam.run(steps,viruses_per_month = virus_config['viruses_per_month'], raxml_time_limit = virus_config['raxml_time_limit'])
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) 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) if params.HA1: signal_peptide = 17 virus_config, epitope_mask, receptor_binding_sites = shift_cds(3*signal_peptide, virus_config, epitope_mask, receptor_binding_sites) # add all arguments to virus_config (possibly overriding) virus_config.update(params.__dict__) # pass all these arguments to the processor: will be passed down as kwargs through all classes myH1N1 = H1N1_process(**virus_config) if params.test: myH1N1.load() else: myH1N1.run(steps,viruses_per_month = virus_config['viruses_per_month'], raxml_time_limit = virus_config['raxml_time_limit'])
num_date = round(lt.tm_year + (lt.tm_yday - 1.0) / 365.0, 2)
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])
else:
params.time_interval = (1995, 2009.5)
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)
# modify clade designations
if not params.ATG:
virus_config, epitope_mask, receptor_binding_sites = shift_cds(
3 * sp, virus_config, epitope_mask, receptor_binding_sites)
# add all arguments to virus_config (possibly overriding)
virus_config.update(params.__dict__)
# pass all these arguments to the processor: will be passed down as kwargs through all classes
myH1N1 = H1N1_process(**virus_config)
if params.test:
myH1N1.load()
else:
myH1N1.run(steps,
viruses_per_month=virus_config['viruses_per_month'],
raxml_time_limit=virus_config['raxml_time_limit'])
lt = time.localtime()
num_date = round(lt.tm_year + (lt.tm_yday - 1.0) / 365.0, 2)
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)
if params.HA1:
signal_peptide = 17
virus_config, epitope_mask, receptor_binding_sites = shift_cds(
3 * signal_peptide, virus_config, epitope_mask,
receptor_binding_sites)
# add all arguments to virus_config (possibly overriding)
virus_config.update(params.__dict__)
# pass all these arguments to the processor: will be passed down as kwargs through all classes
myH1N1 = H1N1_process(**virus_config)
if params.test:
myH1N1.load()
else:
myH1N1.run(steps,
viruses_per_month=virus_config['viruses_per_month'],
raxml_time_limit=virus_config['raxml_time_limit'])
