def TranslateNode(node, tree, terminals, options):
if options.do_translate:
return options.separator.join(sorted(TreeTools.GetLeaves(tree, node)))
elif node in terminals:
return tree.node(node).data.taxon
else:
return str(node)
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv is None:
argv = sys.argv
parser = E.OptionParser(version="%prog version: $Id: trees2tree.py 2782 2009-09-10 11:40:29Z andreas $",
usage=globals()["__doc__"])
parser.add_option("-m", "--method", dest="method", type="choice",
choices=("counts", "min", "max", "sum", "mean", "median", "stddev", "non-redundant", "consensus",
"select-largest"),
help="aggregation function.")
parser.add_option("-r", "--regex-id", dest="regex_id", type="string",
help="regex pattern to extract identifier from tree name for the selection functions.")
parser.add_option("-w", "--write-values", dest="write_values", type="string",
help="if processing multiple trees, write values to file.")
parser.add_option("-e", "--error-branchlength", dest="error_branchlength", type="float",
help="set branch length without counts to this value.")
parser.set_defaults(
method="mean",
regex_id=None,
filtered_branch_lengths=(-999.0, 999.0),
write_values = None,
error_branchlength = None,
separator=":",
)
(options, args) = E.Start(parser, add_pipe_options=True)
if options.loglevel >= 2:
options.stdlog.write("# reading trees from stdin.\n")
options.stdlog.flush()
nexus = TreeTools.Newick2Nexus(sys.stdin)
if options.loglevel >= 1:
options.stdlog.write(
"# read %i trees from stdin.\n" % len(nexus.trees))
nskipped = 0
ninput = len(nexus.trees)
noutput = 0
nerrors = 0
if options.method == "non-redundant":
# compute non-redudant trees
template_trees = []
template_counts = []
ntree = 0
for tree in nexus.trees:
for x in range(0, len(template_trees)):
is_compatible, reason = TreeTools.IsCompatible(
tree, template_trees[x])
if is_compatible:
template_counts[x] += 1
break
else:
template_counts.append(1)
template_trees.append(tree)
if options.loglevel >= 2:
options.stdlog.write(
"# tree=%i, ntemplates=%i\n" % (ntree, len(template_trees)))
ntree += 1
for x in range(0, len(template_trees)):
if options.loglevel >= 1:
options.stdlog.write("# tree: %i, counts: %i, percent=%5.2f\n" %
(x, template_counts[x], template_counts[x] * 100.0 / ntotal))
options.stdout.write(
TreeTools.Tree2Newick(template_trees[x]) + "\n")
elif options.method in ("select-largest",):
# select one of the trees with the same name.
clusters = {}
for x in range(0, len(nexus.trees)):
n = nexus.trees[x].name
if options.regex_id:
n = re.search(options.regex_id, n).groups()[0]
if n not in clusters:
clusters[n] = []
clusters[n].append(x)
new_trees = []
for name, cluster in clusters.items():
new_trees.append(
getBestTree([nexus.trees[x] for x in cluster], options.method))
for x in range(0, len(new_trees)):
options.stdout.write(">%s\n" % new_trees[x].name)
options.stdout.write(TreeTools.Tree2Newick(new_trees[x],) + "\n")
noutput += 1
nskipped = ntotal - noutput
elif options.method == "consensus":
phylip = WrapperPhylip.Phylip()
phylip.setLogLevel(options.loglevel - 2)
phylip.setProgram("consense")
phylip_options = []
phylip_options.append("Y")
phylip.setOptions(phylip_options)
phylip.setTrees(nexus.trees)
result = phylip.run()
options.stdout.write(
"# consensus tree built from %i trees\n" % (phylip.mNInputTrees))
options.stdout.write(
TreeTools.Tree2Newick(result.mNexus.trees[0]) + "\n")
noutput = 1
else:
if options.method in ("min", "max", "sum", "mean", "counts"):
xtree = nexus.trees[0]
for n in xtree.chain.keys():
if xtree.node(n).data.branchlength in options.filtered_branch_lengths:
xtree.node(n).data.branchlength = 0
ntotals = [1] * len(xtree.chain.keys())
if options.method == "min":
f = min
elif options.method == "max":
f = max
elif options.method == "sum":
f = lambda x, y: x + y
elif options.method == "mean":
f = lambda x, y: x + y
elif options.method == "counts":
f = lambda x, y: x + 1
for n in xtree.chain.keys():
if xtree.node(n).data.branchlength not in options.filtered_branch_lengths:
xtree.node(n).data.branchlength = 1
else:
xtree.node(n).data.branchlength = 0
else:
raise "unknown option %s" % options.method
for tree in nexus.trees[1:]:
for n in tree.chain.keys():
if tree.node(n).data.branchlength not in options.filtered_branch_lengths:
xtree.node(n).data.branchlength = f(
xtree.node(n).data.branchlength, tree.node(n).data.branchlength)
ntotals[n] += 1
if options.method == "mean":
for n in xtree.chain.keys():
if ntotals[n] > 0:
xtree.node(n).data.branchlength = float(
xtree.node(n).data.branchlength) / ntotals[n]
else:
if options.error_branchlength is not None:
xtree.node(
n).data.branchlength = options.error_branchlength
if options.loglevel >= 1:
options.stdlog.write(
"# no counts for node %i - set to %f\n" % (n, options.error_branchlength))
nerrors += 1
else:
raise "no counts for node %i" % n
else:
# collect all values for trees
values = [[] for x in range(TreeTools.GetSize(nexus.trees[0]))]
for tree in nexus.trees:
for n, node in tree.chain.items():
if node.data.branchlength not in options.filtered_branch_lengths:
values[n].append(node.data.branchlength)
tree = nexus.trees[0]
for n, node in tree.chain.items():
if len(values[n]) > 0:
if options.method == "stddev":
node.data.branchlength = scipy.std(values[n])
elif options.method == "median":
node.data.branchlength = scipy.median(values[n])
else:
if options.error_branchlength is not None:
node.data.branchlength = options.error_branchlength
if options.loglevel >= 1:
options.stdlog.write(
"# no counts for node %i - set to %f\n" % (n, options.error_branchlength))
nerrors += 1
else:
raise "no counts for node %i" % n
if options.write_values:
outfile = open(options.write_values, "w")
for n, node in tree.chain.items():
values[n].sort()
id = options.separator.join(
sorted(TreeTools.GetLeaves(tree, n)))
outfile.write("%s\t%s\n" %
(id, ";".join(map(str, values[n]))))
outfile.close()
del nexus.trees[1:]
options.stdout.write(TreeTools.Nexus2Newick(nexus) + "\n")
noutput = 1
if options.loglevel >= 1:
options.stdlog.write("# ntotal=%i, nskipped=%i, noutput=%i, nerrors=%i\n" % (
ninput, nskipped, noutput, nerrors))
E.Stop()
