from optparse import OptionParser
from spruce.unrooted import *
from spruce.metrics import *
from spruce.mrp import readTreesFromRatchet
from newick_modified import parse_tree
desc = ' '.join(['This script prints the FP rate, FN rate, and Robinson-Foulds',
'distance between a pair of trees. Each tree must be',
'specified in Newick format.'])
parser = OptionParser(usage = "usage: %prog [options]", description = desc)
parser.add_option("-t", "--true", dest = "true_tree", help = "read true tree from FILE", metavar = "FILE")
parser.add_option("-e", "--estimate", dest = "estimate_tree", help = "read estimate tree from FILE", metavar = "FILE")
(options, args) = parser.parse_args()
if (options.estimate_tree == None or options.true_tree == None):
parser.error("values for both options must be specified\ntry running with the --help flag")
try:
trueTree = readNewickFile(options.true_tree)
except:
trueTree = parse_tree(readTreesFromRatchet(options.true_tree)[0])
try:
estimateTree = readNewickFile(options.estimate_tree)
except:
estimateTree = parse_tree(readTreesFromRatchet(options.estimate_tree)[0])
print getFpFnRfRates(trueTree, estimateTree)
parser = OptionParser(usage="usage: %prog [options]", description=desc)
parser.add_option("-t",
"--true",
dest="true_tree",
help="read true tree from FILE",
metavar="FILE")
parser.add_option("-e",
"--estimate",
dest="estimate_tree",
help="read estimate tree from FILE",
metavar="FILE")
(options, args) = parser.parse_args()
if (options.estimate_tree == None or options.true_tree == None):
parser.error(
"values for both options must be specified\ntry running with the --help flag"
)
try:
trueTree = readNewickFile(options.true_tree)
except:
trueTree = parse_tree(readTreesFromRatchet(options.true_tree)[0])
try:
estimateTree = readNewickFile(options.estimate_tree)
except:
estimateTree = parse_tree(readTreesFromRatchet(options.estimate_tree)[0])
print getFpFnRfRates(trueTree, estimateTree)
#!/usr/bin/env python
from newick_modified import parse_tree
from spruce.unrooted import restrict, readMultipleTreesFromFile
trees = [
parse_tree(tree)
for tree in readMultipleTreesFromFile('kennedy.source_trees')
]
taxaToRemove = set([
'Pelecanus erythrorhynchos', 'Sula bassana', 'Phalacrocorax aristoteles',
'Larus dominicanus', 'Stictocarbo punctatus', 'Fregata minor',
'Fregata ariel', 'Fregata magnificens'
])
for i in range(len(trees)):
trees[i] = restrict(trees[i],
set(trees[i].get_leaves_identifiers()) - taxaToRemove)
f = open('kennedy.source_trees_manual', 'w')
for tree in trees:
f.write(str(tree))
f.write(';\n')
f.close()