def readmany(data, format="newick"):
"""Iterate over trees from a source."""
if type(data) in types.StringTypes:
if os.path.isfile(data):
data = open(data)
else:
data = StringIO(data)
if format == "newick":
for line in data:
yield newick.parse(line)
elif format == "nexus":
for rec in newick.nexus_iter(data):
yield rec.parse()
else:
raise Exception, "format '%s' not recognized" % format
data.close()
def read(data, format=None, treename=None, ttable=None):
"""
Read a single tree from *data*, which can be a Newick string, a
file name, or a file-like object with `tell` and 'read`
methods. *treename* is an optional string that will be attached to
all created nodes.
Args:
data: A file or file-like object or newick string
Returns:
Node: The root node.
"""
import newick
StringTypes = types.StringTypes
def strip(s):
fname = os.path.split(s)[-1]
head, tail = os.path.splitext(fname)
tail = tail.lower()
if tail in (".nwk", ".tre", ".tree", ".newick", ".nex"):
return head
else:
return fname
if (not format):
if (type(data) in StringTypes) and os.path.isfile(data):
s = data.lower()
for tail in ".nex", ".nexus", ".tre":
if s.endswith(tail):
format="nexus"
break
if (not format):
format = "newick"
if format == "newick":
if type(data) in StringTypes:
if os.path.isfile(data):
treename = strip(data)
return newick.parse(file(data), treename=treename,
ttable=ttable)
else:
return newick.parse(data, ttable=ttable)
elif (hasattr(data, "tell") and hasattr(data, "read")):
treename = strip(getattr(data, "name", None))
return newick.parse(data, treename=treename, ttable=ttable)
elif format == "nexus-dendropy":
import dendropy
if type(data) in StringTypes:
if os.path.isfile(data):
treename = strip(data)
return newick.parse(
str(dendropy.Tree.get_from_path(data, "nexus")),
treename=treename
)
else:
return newick.parse(
str(dendropy.Tree.get_from_string(data, "nexus"))
)
elif (hasattr(data, "tell") and hasattr(data, "read")):
treename = strip(getattr(data, "name", None))
return newick.parse(
str(dendropy.Tree.get_from_stream(data, "nexus")),
treename=treename
)
else:
pass
elif format == "nexus":
if type(data) in StringTypes:
if os.path.isfile(data):
with open(data) as infile:
rec = newick.nexus_iter(infile).next()
if rec: return rec.parse()
else:
rec = newick.nexus_iter(StringIO(data)).next()
if rec: return rec.parse()
else:
rec = newick.nexus_iter(data).next()
if rec: return rec.parse()
else:
# implement other tree formats here (nexus, nexml etc.)
raise IOError, "format '%s' not implemented yet" % format
raise IOError, "unable to read tree from '%s'" % data