def china_chicken_0313(taxons, args):
'Find china chicken before 03/2013'
always_in =droplist.do_not_remove()
always_in.extend(droplist.h7n9_all())
taxons = filt_taxon_by_time(taxons, args.stringent_h9n2, args.stringent_h7n9)
taxons = filt_taxon_by_location(taxons, always_in)
taxons = filt_taxon_by_host(taxons, always_in)
return taxons
def filt_taxon_by_time(taxons, h9n2_before_april=False, h7n9_before_april=False):
'''
Take a tree file (dendropy format)
return droplist
False/False -> strip H9N2 in 2014, strip all H7N9
True/True -> strip H9N2 and H7N9 before Aripl 2013
'''
lbs=[lb for lb in taxons if not lb.endswith('2014')] # remove 2014
if h9n2_before_april: # drop taxon list
# due to the fact that i remove duplicats in my process
# and changed chichen, Chicken and ChiCken to chicken.
h9n2 =droplist.h9n2()
h9n2.extend([l.replace('Chicken','chicken') for l in h9n2]) # one capital C
h9n2.extend([l.replace('ChiCken','chicken') for l in h9n2]) # two capital C
lbs =[lb for lb in lbs if not lb in h9n2]
# filt by h7
if h7n9_before_april: # drop post-march 2013
lbs =[lb for lb in lbs if not lb in droplist.h7n9_part2()]
else: # drop all
lbs =[lb for lb in lbs if not lb in droplist.h7n9_all()]
return lbs
def add_h7n9_label(tree):
for ts in tree.taxon_set:
if ts.label in droplist.h7n9_all():
ts.label = ts.label + ' *H7N9* '
return tree