def __init__(
self,
infile=None,
file_format='fasta',
name=None,
datatype=None,
headers=[],
sequences=[],
dv=None,
tree=None,
tmpdir=None,
):
self.TCfiles = {}
self.dv = dv or []
if tree and isinstance(tree, Tree):
self.tree = TrClTree.cast(tree)
else:
self.tree = None
super(TrClSeq, self).__init__(
infile,
file_format,
name,
datatype,
headers,
sequences,
tmpdir,
)
def tree_collection(self):
""" Uses TreeCollection (via
treeCl.externals.tree_builders.TreeCollection) to build a least squares
tree for the current record """
if self.dv <= []:
self.dv_matrix()
tc = TreeCollection(self)
self.tree = TrClTree.cast(tc.run())
def tree_collection(self):
""" Uses TreeCollection (via
treeCl.externals.tree_builders.TreeCollection) to build a least squares
tree for the current record """
if self.dv <= []:
self.dv_matrix()
tc = TreeCollection(self)
self.tree = TrClTree.cast(tc.run())
def bionj_plus(self):
""" Uses phyml (via treeCl.externals.tree_builders.Phyml) to build a
bioNJ tree for the current record """
if self.tmpdir is not None:
tmpdir = self.tmpdir
else:
directorycheck(tmpdir)
p = Phyml(self)
self.tree = TrClTree.cast(p.run('lr'))
def phyml(self, tmpdir):
""" Uses phyml (via treeCl.externals.tree_builders.Phyml) to build a
full ML tree for the current record """
if self.tmpdir is not None:
tmpdir = self.tmpdir
else:
directorycheck(tmpdir)
p = Phyml(self, tmpdir)
self.tree = TrClTree.cast(p.run('ml'))
def bionj(self, tmpdir, verbosity=0):
""" Uses phyml (via treeCl.externals.tree_builders.Phyml) to build a
bioNJ tree for the current record """
if self.tmpdir is not None:
tmpdir = self.tmpdir
else:
directorycheck(tmpdir)
p = Phyml(self, tmpdir)
self.tree = TrClTree.cast(p.run('nj', verbosity))
return self.tree
def tree_collection(self, tmpdir):
""" Uses TreeCollection (via
treeCl.externals.tree_builders.TreeCollection) to build a least squares
tree for the current record """
if self.tmpdir is not None:
tmpdir = self.tmpdir
else:
directorycheck(tmpdir)
if self.dv <= []:
self.dv_matrix()
tc = TreeCollection(self, tmpdir)
self.tree = TrClTree.cast(tc.run())
def tree_collection_deprecated(self, tmpdir):
""" DEPRECATED: Uses TreeCollection (via
treeCl.software_interfaces.treecollection) to build a least squares
tree for the current record """
if self.tmpdir is not None:
tmpdir = self.tmpdir
else:
directorycheck(tmpdir)
if self.dv <= []:
self.dv_matrix()
tc = TreeCollection(self, tmpdir)
self.tree = TrClTree.cast(tc.run())
def bionj(self):
""" Uses phyml (via treeCl.externals.tree_builders.Phyml) to build a
bioNJ tree for the current record """
p = Phyml(self)
self.tree = TrClTree.cast(p.run('nj'))
def phyml(self):
""" Uses phyml (via treeCl.externals.tree_builders.Phyml) to build a
full ML tree for the current record """
p = Phyml(self)
self.tree = TrClTree.cast(p.run('ml'))
def bionj(self):
""" Uses phyml (via treeCl.externals.tree_builders.Phyml) to build a
bioNJ tree for the current record """
p = Phyml(self)
self.tree = TrClTree.cast(p.run('nj'))
def phyml(self):
""" Uses phyml (via treeCl.externals.tree_builders.Phyml) to build a
full ML tree for the current record """
p = Phyml(self)
self.tree = TrClTree.cast(p.run('ml'))