def write(self, features=None, outfile=None, format=10):
"""
Inherits from Tree but adds the tenth format, that allows to display marks for CodeML.
TODO: internal writting format need to be something like 0
"""
from re import sub
if int(format)==11:
nwk = ' %s 1\n' % (len(self))
nwk += sub('\[&&NHX:mark=([ #0-9.]*)\]', r'\1', \
write_newick(self, features=['mark'],format=9))
elif int(format)==10:
nwk = sub('\[&&NHX:mark=([ #0-9.]*)\]', r'\1', \
write_newick(self, features=['mark'],format=9))
else:
nwk = write_newick(self, features=features,format=format)
if outfile is not None:
open(outfile, "w").write(nwk)
return nwk
else:
return nwk
def write(self, features=None, outfile=None, format=10):
"""
Inherits from Tree but adds the tenth format, that allows to display marks for CodeML.
TODO: internal writting format need to be something like 0
"""
from re import sub
if int(format) == 11:
nwk = ' %s 1\n' % (len(self))
nwk += sub('\[&&NHX:mark=([ #0-9.]*)\]', r'\1', \
write_newick(self, features=['mark'],format=9))
elif int(format) == 10:
nwk = sub('\[&&NHX:mark=([ #0-9.]*)\]', r'\1', \
write_newick(self, features=['mark'],format=9))
else:
nwk = write_newick(self, features=features, format=format)
if outfile is not None:
open(outfile, "w").write(nwk)
return nwk
else:
return nwk
n.remove_child(child)
for grandchild in child.children:
n.add_child(grandchild)
num_collapsed += 1
msg = ''
if num_collapsed:
msg = 'Collapsed {} internal branch{}'.format(
num_collapsed, 'es' if num_collapsed > 1 else '')
if num_set_zero_tip:
if msg:
msg += ', set {} external branch{} to zero'.format(
num_set_zero_tip, 'es' if num_set_zero_tip > 1 else '')
else:
msg += 'Set {} external branch{} to zero'.format(
num_set_zero_tip, 'es' if num_set_zero_tip > 1 else '')
if num_set_zero_root:
if msg:
msg += ', set {} root child branch{} to zero'.format(
num_set_zero_root, 'es' if num_set_zero_root > 1 else '')
else:
msg += 'Set {} root child branch{} to zero'.format(
num_set_zero_root, 'es' if num_set_zero_root > 1 else '')
if not msg:
msg = 'Did not find any branches to modify'
logging.info('{} (criterion: {} <{} {}).'.format(
msg, params.feature, '' if params.strict else '=', threshold))
nwk = write_newick(tr, format_root_node=True, format=1)
with open(params.output_tree, 'w+') as f:
f.write('%s\n' % nwk)