def get_tree(self):
matrix = matrixRepresentation(self.trees)
if (len(matrix[0]) == 0 or len(matrix[1]) == 0):
return (str(Tree()))
f = tempfile.NamedTemporaryFile()
prefix = f.name
f.close()
f = open(prefix, 'w')
writeRatchetInputFile(matrix,
f,
filePrefix=prefix,
numRatchetIterations=self.numIters)
f.close()
pipe = Popen("paup -n %s" % prefix,
shell=True,
stdout=PIPE,
stderr=PIPE)
(out, err) = pipe.communicate()
if self.mrpType == 'gmrp':
trees = getConsensusTreesFromPaupFiles(prefix)
output = trees['gmrp']
elif self.mrpType == 'rmrp':
mpTrees = readTreesFromRatchet(prefix + '.tre')
output = random.choice(mpTrees)
os.remove(prefix)
os.remove(prefix + ".log")
os.remove(prefix + ".gmrp")
os.remove(prefix + ".smrp")
os.remove(prefix + ".mmrp")
os.remove(prefix + ".tre")
os.remove(prefix + ".tre.nex")
return output
## You should have received a copy of the GNU General Public License
## along with spruce. If not, see <http://www.gnu.org/licenses/>.
###########################################################################
from optparse import OptionParser
from spruce.unrooted import *
from spruce.metrics import *
from spruce.mrp import readTreesFromRatchet, getGreedyConsensus
from newick_modified.lexer import LexerError
desc = ' '.join(['This script prints the greedy consensus of a set of trees, as',
'calculated by PAUP*. Trees must be specified in Newick',
'format.'])
parser = OptionParser(usage = "usage: %prog [options]", description = desc)
parser.add_option("-t", "--trees", dest = "estimate_tree", help = "read supertrees from FILE", metavar = "FILE")
parser.add_option("-s", "--sources", dest = "sources_file", help = "read source trees from FILE", metavar = "FILE")
(options, args) = parser.parse_args()
if (options.estimate_tree == None or options.sources_file == None):
parser.error("values for both options must be specified\ntry running with the --help flag")
sourceTrees = [parse_tree(source) for source in readMultipleTreesFromFile(options.sources_file)]
try:
supertrees = [parse_tree(estimate) for estimate in readMultipleTreesFromFile(options.estimate_tree)]
except LexerError:
supertrees = [parse_tree(estimate) for estimate in readTreesFromRatchet(options.estimate_tree)]
lines = getGreedyConsensus(sourceTrees, supertrees, rooted = True)
print ''.join(lines), '\n'
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)
metavar="FILE")
parser.add_option("-s",
"--sources",
dest="sources_file",
help="read source trees from FILE",
metavar="FILE")
(options, args) = parser.parse_args()
if (options.estimate_tree == None or options.sources_file == None):
parser.error(
"values for both options must be specified\ntry running with the --help flag"
)
sourceTrees = [
parse_tree(source)
for source in readMultipleTreesFromFile(options.sources_file)
]
try:
supertrees = [
parse_tree(estimate)
for estimate in readMultipleTreesFromFile(options.estimate_tree)
]
except LexerError:
supertrees = [
parse_tree(estimate)
for estimate in readTreesFromRatchet(options.estimate_tree)
]
lines = getGreedyConsensus(sourceTrees, supertrees, rooted=True)
print ''.join(lines), '\n'
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)