def _validate_arguments_to_add_state(self, ms, m_name):
"""
makes sure the add_motif function is called correctly
:param m: motif to add to tree
:type m: Motif object
:param m_name: name of motif to add
:type m_name: str
:return: None
"""
if ms is not None and m_name is not None:
raise exceptions.MotifStateTreeException(
"cannot supply both a state and motif name to add a state to "
"a motif state tree")
if ms is None and m_name is None:
raise exceptions.MotifStateTreeException(
"must supply a motif state object or motif name to add_state")
if ms is not None:
for n in self.tree.nodes:
if n.data.ref_state.uuid == ms.uuid:
raise exceptions.MotifStateTreeException(
"cannot add state: " + ms.name +
" to tree as its uuid is " +
"already present in the tree")
def add_mst(self,
mst,
parent_index=-1,
parent_end_index=-1,
parent_end_name=None):
parent = self._get_parent_node(parent_index)
parent_avail_ends = self._get_parent_available_ends(
parent, parent_end_index, parent_end_name)
if len(parent_avail_ends) > 1 or len(parent_avail_ends) == 0:
parent_end_index = -1
else:
parent_end_index = parent_avail_ends[0]
index_dict = {}
for i, n in enumerate(mst):
if i == 0:
j = self.add_state(n.data.ref_state, parent_index,
parent_end_index)
else:
ind = index_dict[n.parent_index()]
pei = n.parent_end_index()
j = self.add_state(n.data.ref_state,
parent_index=ind,
parent_end_index=pei)
if j == -1:
raise exceptions.MotifStateTreeException(
"failed to add a state in add_mst to the current "
"motif tree it is likely a steric clash, consider "
"turning off sterics")
index_dict[n.index] = j
def _get_state_from_manager(self, m_name, m_end_name):
"""
helper function for add_motif should not be called directly. calls
resource manager to get motif to be added to tree by the name of
the motif.
:param m_name: name of the motif to add to the tree
:type m_name: str
:param m_end_name: name of the basepair end of the motif to align by.
:type m_end_name: str
"""
try:
if m_end_name is not None:
state = rm.manager.get_state(name=m_name, end_name=m_end_name)
else:
state = rm.manager.get_state(name=m_name)
except exceptions.ResourceManagerException as e:
raise exceptions.MotifStateTreeException(
"cannot add state to tree, state cannot be found in resource "
"manager")
return state
def get_node(self, i=None, uuid=None):
if i is not None:
return self.tree.get_node(i)
elif uuid is not None:
for n in self.tree:
if n.data.cur_state.uuid == uuid:
return n
raise exceptions.MotifStateTreeException(
"cannot find motif state with uuid")
def _get_connection_end(self, node, bp_name):
node_end_index = -1
if bp_name != "":
ei = node.data.get_end_index(name=bp_name)
if not node.available_pos(ei):
raise exceptions.MotifStateTreeException(
"cannot add connection with " + str(node.index) + " and "
"end name " + bp_name + " as this end is not available")
if self.connections.in_connection(node.index, bp_name):
raise exceptions.MotifStateTreeException(
"cannot add connection with " + node.index + " and end "
"name " + bp_name + " as this end is already in a "
"connection")
node_end_index = ei
else:
node_indexes = node.available_children_pos()
node_indexes.remove(0)
if len(node_indexes) > 1:
raise exceptions.MotifStateTreeException(
"cannot connect nodes " + str(node.index) + " its unclear "
" which ends to attach")
if len(node_indexes) == 0:
raise exceptions.MotifStateTreeException(
"cannot connect nodes " + str(node.index) + " there are "
"no ends free ends to attach too")
node_index_name = node.data.cur_state.end_names[node_indexes[0]]
if self.connections.in_connection(node.index, node_index_name):
raise exceptions.MotifStateTreeException(
"cannot add connection with " + str(node.index) +
" and end "
"name " + node_index_name + " as this end is already in a "
"connection")
node_end_index = node_indexes[0]
return node_end_index
def _get_parent_node(self, parent_index):
"""
gets node that serve as the parent of the current motif being added
to the tree.
:param parent_index: the tree index corresponding to the requested motif
:type parent_index: int
:return: tree node of parent
:rtype: TreeNode
"""
parent = self.tree.last_node
if parent_index != -1:
try:
parent = self.tree.get_node(parent_index)
except exceptions.TreeIndexException:
raise exceptions.MotifStateTreeException(
"parent_index supplied: " + str(parent_index) +
" does not " + "exist in current motif state tree")
return parent
def _get_parent_available_ends(self, parent, parent_end_index,
parent_end_name):
"""
Gets the available ends of the parent that the current motif can align
to. If either parent_end_index or parent_end_name are specified, checks
to see if that position is available.
:param parent: the TreeNode of parent
:type parent: TreeNode
:param parent_end_index: which end this motif will be aligned to on
parent
:type parent_end_index: int
:param parent_end_name: the name instead of the index of the end the
current motif will align to
:type parent_end_name: str
:return: list of available parent end indexes that meet the specified
constraints
:rtype: list of ints
"""
if parent is None:
return []
if parent_end_index != -1 and parent_end_name is not None:
raise exceptions.MotifStateTreeException(
"cannot supply parent_end_index and parent_end_name together")
elif parent_end_name is not None:
try:
parent_end_index = parent.data.get_end_index(
name=parent_end_name)
except:
raise exceptions.MotifStateTreeException(
"cannot find parent_end_name: " + parent_end_name + " in "
"parent motif: " + parent.data.name())
if parent_end_index == parent.data.block_end_add():
raise exceptions.MotifStateTreeException(
"cannot add state: to tree as the parent_end_name" +
" supplied is blocked see class MotifState")
available = parent.available_pos(parent_end_index)
if not available:
raise exceptions.MotifStateTreeException(
"cannot add state to tree as the end " +
"you are trying to add it to is already filled or does "
"not exist")
if self.connections.in_connection(parent.index, parent_end_name):
raise exceptions.MotifStateTreeException(
"cannot add motif to tree as the end " +
"you are trying to add it to is in a connection")
return [parent_end_index]
elif parent_end_index != -1:
if parent_end_index == parent.data.block_end_add():
raise exceptions.MotifStateTreeException(
"cannot add state: to tree as the parent_end_index" +
" supplied is blocked see class MotifState")
available = parent.available_pos(parent_end_index)
if not available:
raise exceptions.MotifStateTreeException(
"cannot add state to tree as the end " +
"you are trying to add it to is already filled or does "
"not exist")
parent_end_name = parent.data.cur_state.end_names[parent_end_index]
if self.connections.in_connection(parent.index, parent_end_name):
raise exceptions.MotifStateTreeException(
"cannot add motif to tree as the end " +
"you are trying to add it to is in a connection")
return [parent_end_index]
else:
avail_pos = parent.available_children_pos()
avail_pos.remove(0)
final_avail_pos = []
for p in avail_pos:
pen = parent.data.cur_state.end_names[p]
if self.connections.in_connection(parent.index, pen):
continue
if p == parent.data.block_end_add:
continue
final_avail_pos.append(p)
return final_avail_pos