def __format__(self, format_spec):
"""Serialize the tree as a string in the specified file format.
This method supports the format() built-in function added in Python
2.6/3.0. The format_spec should be a lower case string supported by
Bio.Phylo.write as an output file format.
"""
if format_spec:
from StringIO import StringIO
from Bio.Phylo import _io
handle = StringIO()
_io.write([self], handle, format_spec)
return handle.getvalue()
else:
# Follow python convention and default to using __str__
return str(self)
def __format__(self, format_spec):
"""Serialize the tree as a string in the specified file format.
This method supports Python's ``format`` built-in function.
:param format_spec: a lower-case string supported by ``Bio.Phylo.write``
as an output file format.
"""
if format_spec:
from io import StringIO
from Bio.Phylo import _io
handle = StringIO()
_io.write([self], handle, format_spec)
return handle.getvalue()
else:
# Follow python convention and default to using __str__
return str(self)
def parseChain(lnfchains,
dold2newname={},
nfchainout=None,
inchainfmt='nexus',
outchainfmt='newick',
verbose=False):
"""parse a Nexus-format tree chain and re-write it in a Newick format; edit the tree on the fly, substituting tip labels or grafting trees on tips"""
if verbose: print "parseChain('%s')" % repr(lnfchains)
ntree = 0
buffsize = 50
treebuffer = []
if nfchainout: nfout = nfchainout
else:
nfout = n2outChainFileName(lnfchains[0], dirout, inchainfmt,
outchainfmt)
dhandles = {}
for k, nfchain in enumerate(lnfchains):
dhandles[k] = PhyloIO.parse(nfchain, inchainfmt)
# intertwines the trees from separate chains, respecting their sequence
# so that the burn-in can still be defined as the first portion of trees in the sample.
sometreeleft = True
ichains = range(len(lnfchains))
while sometreeleft:
for k in ichains:
#~ sys.stdout.write('\rk'+str(k)) ; sys.stdout.flush()
try:
tree = dhandles[k].next()
#~ print tree
#~ sys.stdout.flush()
except StopIteration:
sometreeleft = False
# stops for all chains here, even if they had different length (which shoulld not be)
break # the for k loop
if dold2newname:
for tip in tree.get_terminals():
nutipname = dold2newname.get(tip.name)
if nutipname:
if isinstance(nutipname, str):
tip.name = nutipname
else:
if isinstance(nutipname, tree2.Node):
nusubtree = tree2toBioPhylo(nutipname)
elif isinstance(nutipname, BaseTree.TreeElement):
nusubtree = nutipname
else:
raise ValueError, "replacement value for a leaf must be either a string (to edit leaf label) of a tree object instance of classes tree2.Node or Bio.Phylo.TreeElement (or derivates)"
subtreelen = nusubtree.total_branch_length(
) / nusubtree.count_terminals()
if subtreelen:
# substract the subtree length to its branch length
tip.branch_length = max(
0.0, tip.branch_length - subtreelen)
# attach subtree to tree
tip.clades = nusubtree.root.clades
tip.name = ''
treebuffer.append(tree)
ntree += 1
#~ sys.stdout.write('\rntree'+str(ntree)) ; sys.stdout.flush()
if len(treebuffer) >= buffsize:
if verbose:
sys.stdout.write('\r' + str(ntree))
sys.stdout.flush()
if ntree <= buffsize:
PhyloIO.write(treebuffer, nfout, outchainfmt)
else:
treeappend(treebuffer, nfout, outchainfmt)
treebuffer = []
if treebuffer: treeappend(treebuffer, nfout, outchainfmt)
print '%s%s ...done (%d trees)' % (('\n' if verbose else ''), nfout, ntree)
return None
