def Process(lines, other_trees, options, map_old2new, ntree):
nexus = TreeTools.Newick2Nexus(map(lambda x: x[:-1], lines))
if options.loglevel >= 1:
options.stdlog.write("# read %i trees.\n" % len(nexus.trees))
nskipped = 0
ntotal = len(nexus.trees)
extract_pattern = None
species2remove = None
write_map = False
phylip_executable = None
phylip_options = None
index = 0
# default: do not output internal node names
write_all_taxa = False
for tree in nexus.trees:
if options.outgroup:
tree.root_with_outgroup(options.outgroup)
for method in options.methods:
if options.loglevel >= 3:
options.stdlog.write("# applying method %s to tree %i.\n" %
(method, index))
if method == "midpoint-root":
tree.root_midpoint()
elif method == "balanced-root":
tree.root_balanced()
elif method == "unroot":
TreeTools.Unroot(tree)
elif method == "phylip":
if not phylip_executable:
phylip_executable = options.parameters[0]
del options.parameters[0]
phylip_options = re.split("@", options.parameters[0])
del options.parameters[0]
phylip = WrapperPhylip.Phylip()
phylip.setProgram(phylip_executable)
phylip.setOptions(phylip_options)
phylip.setTree(tree)
result = phylip.run()
nexus.trees[index] = result.mNexus.trees[0]
elif method == "normalize":
if options.value == 0:
v = 0
for n in tree.chain.keys():
v = max(v, tree.node(n).data.branchlength)
else:
v = options.value
for n in tree.chain.keys():
tree.node(n).data.branchlength /= float(options.value)
elif method == "divide-by-tree":
if len(other_trees) > 1:
other_tree = other_trees[ntree]
else:
other_tree = other_trees[0]
# the trees have to be exactly the same!!
if options.loglevel >= 2:
print tree.display()
print other_tree.display()
if not tree.is_identical(other_tree):
nskipped += 1
continue
# even if the trees are the same (in topology), the node numbering might not be
# the same. Thus build a map of node ids.
map_a2b = TreeTools.GetNodeMap(tree, other_tree)
for n in tree.chain.keys():
try:
tree.node(n).data.branchlength /= float(
other_tree.node(map_a2b[n]).data.branchlength)
except ZeroDivisionError:
options.stdlog.write(
"# Warning: branch for nodes %i and %i in tree-pair %i: divide by zero\n"
% (n, map_a2b[n], ntree))
continue
elif method == "rename":
if not map_old2new:
map_old2new = IOTools.ReadMap(open(options.parameters[0],
"r"),
columns=(0, 1))
if options.invert_map:
map_old2new = IOTools.getInvertedDictionary(
map_old2new, make_unique=True)
del options.parameters[0]
unknown = []
for n, node in tree.chain.items():
if node.data.taxon:
try:
node.data.taxon = map_old2new[node.data.taxon]
except KeyError:
unknown.append(node.data.taxon)
for taxon in unknown:
tree.prune(taxon)
# reformat terminals
elif method == "extract-with-pattern":
if not extract_pattern:
extract_pattern = re.compile(options.parameters[0])
del options.parameters[0]
for n in tree.get_terminals():
node = tree.node(n)
node.data.taxon = extract_pattern.search(
node.data.taxon).groups()[0]
elif method == "set-uniform-branchlength":
for n in tree.chain.keys():
tree.node(n).data.branchlength = options.value
elif method == "build-map":
# build a map of identifiers
options.write_map = True
for n in tree.get_terminals():
node = tree.node(n)
if node.data.taxon not in map_old2new:
new = options.template_identifier % (len(map_old2new) +
1)
map_old2new[node.data.taxon] = new
node.data.taxon = map_old2new[node.data.taxon]
elif method == "remove-pattern":
if species2remove is None:
species2remove = re.compile(options.parameters[0])
del options.parameters
taxa = []
for n in tree.get_terminals():
t = tree.node(n).data.taxon
skip = False
if species2remove.search(t):
continue
if not skip:
taxa.append(t)
TreeTools.PruneTree(tree, taxa)
elif method == "add-node-names":
inode = 0
write_all_taxa = True
for n, node in tree.chain.items():
if not node.data.taxon:
node.data.taxon = "inode%i" % inode
inode += 1
elif method == "newick2nhx":
# convert names to species names
for n in tree.get_terminals():
t = tree.node(n).data.taxon
d = t.split("|")
if len(d) >= 2:
tree.node(n).data.species = d[0]
index += 1
ntree += 1
if options.output_format == "nh":
options.stdout.write(
TreeTools.Nexus2Newick(
nexus,
write_all_taxa=True,
with_branchlengths=options.with_branchlengths) + "\n")
else:
for tree in nexus.trees:
tree.writeToFile(options.stdout, format=options.output_format)
return ntotal, nskipped, ntree
