need to sort them by the mrcas and then do them all at once
"""
# this will either be sister or will be at a polytomy
add_as_sister = True
if __name__ == "__main__":
if len(sys.argv) != 3:
print "python " + sys.argv[0] + " infile.tre names.txt"
sys.exit(0)
tree = tree_reader.read_tree_file_iter(sys.argv[1]).next()
tree_utils.set_heights(tree)
of = open(sys.argv[2], "r")
replace = {} #key is single mrca taxon, value is node that is to be used
for i in of:
spls = i.strip().split(",")
nms = spls[1:]
nm = spls[0]
x = None
if len(nms) == 1:
if nms[0] in replace:
x = replace[nms[0]]
else:
for j in tree.leaves():
if j.label == nms[0]:
x = j
toremove.append(i)
for i in toremove:
sys.stderr.write("remove internal: "+i.get_newick_repr(False)+"\n")
par = i.parent
par.remove_child(i)
if __name__ == "__main__":
if len(sys.argv) != 3:
print "python "+sys.argv[0]+ " addtree bigtre"
sys.exit(0)
tree1 = tree_reader.read_tree_file_iter(sys.argv[1]).next()
bigtree = tree_reader.read_tree_file_iter(sys.argv[2]).next()
if EDITLEN:
tree_utils.set_heights(tree1)
tree_utils.set_heights(bigtree)
rootnms = set(tree1.lvsnms())
remove_int_ext_nodes(rootnms,bigtree)
othernms = set(bigtree.lvsnms())
if VERBOSE:
ddifs = rootnms.difference(othernms)
for i in ddifs:
sys.stderr.write(i+"\n")
diffnms = []
diffnds = {}
didit = False
nrt = tree_utils.get_mrca_wnms(list(rootnms.intersection(othernms)),bigtree).parent
import os
import tree_reader
import tree_utils
"""
assuming that the datedtre just has ott ids as the tip names
assuming the labelled_supertree has ott in front of the ott ids
"""
if __name__ == "__main__":
if len(sys.argv) != 3:
print "python " + sys.argv[0] + " datedtree labelled_superrtree"
sys.exit(0)
dated = tree_reader.read_tree_file_iter(sys.argv[1]).next()
ott = tree_reader.read_tree_file_iter(sys.argv[2]).next()
tree_utils.set_heights(dated)
ottlvsd = {} #key is name and value is node
for i in ott.iternodes():
ottlvsd[i.label] = i
for i in dated.leaves():
try:
i.data["node"] = ottlvsd[i.label] #ottlvsd["ott"+i.label]
except:
print >> sys.stderr, "not matched", i.label
continue
done = set()
dates = {} # key is node, value is date
dates_names = {} #key is node, value is mrca string
for i in dated.iternodes(order="preorder"):