def convert(fileName, HostOrder, n, writeParasite):
"""takes name of original .newick file and the dictionary of host tree branch lengths
and creates files for the host + parasite trees. Parasite tree can
be ommited if desired"""
f = open(fileName, 'r')
contents = f.read()
f.close()
H, P, phi = contents.split(";")
P = P.strip()
H = "{};" .format(H.strip())
host = treelib1.parse_newick(H, HostOrder)
for key in HostOrder:
H = H.replace(str(key), "{}:{}".format(str(key), str(HostOrder[key])))
f = open("{}{}.stree".format(fileName[:-7], str(n)), 'w')
treelib1.write_newick(host, f, root_data=True)
f.close()
if writeParasite:
f = open("{}.tree".format(fileName[:-7]), 'w')
f.write("{};".format(P))
f.close()
def convert(fileName, HostOrder, n, writeParasite):
"""takes name of original .newick file and the dictionary of host tree branch lengths
and creates files for the host + parasite trees. Parasite tree can
be ommited if desired"""
f = open(fileName, 'r')
contents = f.read()
host, paras, phi = newickFormatReader.getInput(fileName)
hostRoot = cycleCheckingGraph.findRoot(host)
f.close()
H, P, phi = contents.split(";")
P = P.strip()
H = H.strip()
H = H + ';'
host = treelib1.parse_newick(H, HostOrder)
for key in HostOrder:
H = H.replace(str(key), str(key) + ':' + str(HostOrder[key]))
f = open(fileName[:-7] + str(n) + ".stree", 'w')
treelib1.write_newick(host, f, root_data=True)
f.close()
if writeParasite:
f = open(fileName[:-7] + '.tree', 'w')
f.write(P + ";")
f.close()
def convert(fileName, HostOrder, n, writeParasite):
"""takes name of original .newick file and the dictionary of host tree branch lengths
and creates files for the host + parasite trees. Parasite tree can
be ommited if desired"""
f = open(fileName, 'r')
contents = f.read()
host, paras, phi = newickFormatReader.getInput(fileName)
hostRoot = cycleCheckingGraph.findRoot(host)
f.close()
H,P,phi = contents.split(";")
P = P.strip()
H = H.strip()
H = H + ';'
host = treelib1.parse_newick(H, HostOrder)
for key in HostOrder:
H = H.replace(str(key), str(key) + ':' + str(HostOrder[key]))
f = open(fileName[:-7]+ str(n) +".stree", 'w')
treelib1.write_newick(host, f, root_data = True)
f.close()
if writeParasite:
f = open(fileName[:-7] + '.tree', 'w')
f.write(P + ";")
f.close()
