def consensusTree(self, iterations):
import tempfile
from SAP.Bio.Nexus import Trees as NexusTrees
tmpFile, tmpFileName = tempfile.mkstemp()
self.dumpBootstrapTreesNexus(iterations, tmpFileName)
bootstrapTrees = Nexus.Nexus(tmpFileName)
tmpFile.close()
os.remove(tmpFileName)
consensusTree = NexusTrees.consensus(bootstrapTrees.trees)
return "#NEXUS\n\nbegin trees;\n " + consensusTree.to_string() + "\nend;\n"
def consensusTree(self, iterations):
import tempfile
from SAP.Bio.Nexus import Trees as NexusTrees
tmpFile, tmpFileName = tempfile.mkstemp()
self.dumpBootstrapTreesNexus(iterations, tmpFileName)
bootstrapTrees = Nexus.Nexus(tmpFileName)
tmpFile.close()
os.remove(tmpFileName)
consensusTree = NexusTrees.consensus(bootstrapTrees.trees)
return "#NEXUS\n\nbegin trees;\n " + consensusTree.to_string(
) + "\nend;\n"
def run(self, alignmentFileName):
"""
Run neighbour join bootstrap on alignment
Returns name of tree file
"""
baseName = os.path.splitext(os.path.split(alignmentFileName)[-1])[0]
treeFileName = os.path.join(self.options.treescache,
baseName + ".nex.nj.tree")
print "%s: Sampling trees: " % baseName,
sys.stdout.flush()
# TODO: The way we check if there are cached results is not safe. The file may not be complete.
if os.path.exists(treeFileName):
print "Using cached results."
sys.stdout.flush()
else:
print "Computing...",
sys.stdout.flush()
constraintTreeFileName = os.path.join(self.options.homologcache,
baseName + ".nex")
constraintTreeFile = open(constraintTreeFileName, 'r')
constraintTree = Nexus.Nexus(constraintTreeFile).trees[0]
queryName = baseName
alignment = Nexus.Nexus(alignmentFileName)
nj = NeighbourJoin.NeighbourJoin(alignment,
queryName=queryName,
constraintTree=constraintTree)
nj.dumpBootstrapTrees(self.options.bootstraps, treeFileName)
bootstrapTrees = Nexus.Nexus(treeFileName)
consensusTree = NexusTrees.consensus(bootstrapTrees.trees)
consensusTreeFileName = os.path.join(self.options.treescache,
baseName + ".nj.con")
s = "#NEXUS\n\nbegin trees;\n " + consensusTree.to_string(
) + "\nend;\n"
writeFile(consensusTreeFileName, s)
print "done."
sys.stdout.flush()
def run(self, alignmentFileName):
"""
Run neighbour join bootstrap on alignment
Returns name of tree file
"""
baseName = os.path.splitext(os.path.split(alignmentFileName)[-1])[0]
treeFileName = os.path.join(self.options.treescache, baseName + ".nex.nj.tree")
print "%s: Sampling trees: " % baseName,
sys.stdout.flush()
# TODO: The way we check if there are cached results is not safe. The file may not be complete.
if os.path.exists(treeFileName):
print "Using cached results."
sys.stdout.flush()
else:
print "Computing...",
sys.stdout.flush()
constraintTreeFileName = os.path.join(self.options.homologcache, baseName + ".nex")
constraintTreeFile = open(constraintTreeFileName, 'r')
constraintTree = Nexus.Nexus(constraintTreeFile).trees[0]
queryName = baseName
alignment = Nexus.Nexus(alignmentFileName)
nj = NeighbourJoin.NeighbourJoin(alignment, queryName=queryName, constraintTree=constraintTree)
nj.dumpBootstrapTrees(self.options.bootstraps, treeFileName)
bootstrapTrees = Nexus.Nexus(treeFileName)
consensusTree = NexusTrees.consensus(bootstrapTrees.trees)
consensusTreeFileName = os.path.join(self.options.treescache, baseName + ".nj.con")
s = "#NEXUS\n\nbegin trees;\n " + consensusTree.to_string() + "\nend;\n"
writeFile(consensusTreeFileName, s)
print "done."
sys.stdout.flush()
