Exemplo n.º 1
0
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()
Exemplo n.º 2
0
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()
Exemplo n.º 3
0
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()