def _get_connection_end(self, node, bp_name):
node_end_index = -1
if bp_name != "":
ei = node.data.get_end_index(bp_name)
if not node.available_pos(ei):
raise exceptions.MotifGraphException(
"cannot add connection with " + str(node.index) + " and "
"end name " + bp_name + " as this end is not available")
node_end_index = ei
else:
node_indexes = node.available_children_pos()
if len(node_indexes) > 1:
raise exceptions.MotifGraphException("cannot connect nodes " +
str(node.index) +
" its unclear "
" which ends to attach")
if len(node_indexes) == 0:
raise exceptions.MotifGraphException(
"cannot connect nodes " + str(node.index) + " there are "
"no ends free ends to attach too")
node_end_index = node_indexes[0]
return node_end_index
def _validate_arguments_to_add_motif(self, m, m_name):
"""
makes sure the add_motif function is called correctly
:param m: motif to add to graph
:type m: Motif object
:param m_name: name of motif to add
:type m_name: str
:return: None
"""
if m is not None and m_name is not None:
raise exceptions.MotifGraphException(
"cannot supply both a motif and motif name to add a motif to "
"a motif graph")
if m is None and m_name is None:
raise exceptions.MotifGraphException(
"must supply a motif object or motif name to add_motif")
if m is not None:
for n in self.graph.nodes:
if n.data.id == m.id:
raise exceptions.MotifGraphException(
"cannot add motif: " + m.name +
" to graph as its uuid is " +
"already present in the graph")
def _get_motif_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:
m = rm.manager.get_motif(name=m_name, end_name=m_end_name)
else:
m = rm.manager.get_motif(name=m_name)
except exceptions.ResourceManagerException as e:
raise exceptions.MotifGraphException(
"cannot add motif to graph, motif cannot be found in resource "
"manager")
return m
def replace_motif(self, pos, new_motif):
node = self.get_node(pos)
if len(new_motif.ends) != len(node.data.ends):
raise exceptions.MotifGraphException(
"attempted to replace a motif with a different number of ends")
node.data = new_motif.copy()
self.update_merger = 1
self._align_motifs_all_motifs()
def get_node(self, i=None, uuid=None, m_name=None):
if i is not None:
return self.graph.get_node(i)
node = None
for n in self.graph.nodes:
if n.data.id == uuid:
return n
if n.data.name == m_name:
if node is not None:
raise exceptions.MotifGraphException(
"cannot get node with motif name: " + m_name +
" there "
"are more then one")
node = n
if node is None:
raise exceptions.MotifGraphException(
"could not find node with uuid " + str(uuid) +
" and m_name: " + m_name)
return node
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.graph.last_node
if parent_index != -1:
try:
parent = self.graph.get_node(parent_index)
except exceptions.GraphIndexException:
raise exceptions.MotifGraphException(
"parent_index supplied: " + str(parent_index) +
" does not " + "exist in current motif graph")
return parent
def _assign_node_levels(self):
"""
calculates and stores the node level of each node in the mt. The
head node has a level of 1 and its children have a level of 2 and
so on.
"""
nodes = self.mg.get_not_aligned_nodes()
if len(nodes) == 0:
raise exceptions.MotifGraphException(
"cannot find a place to start printing in motif_graph"
" to_pretty_str")
start = nodes[0].index
i = 0
for n in graph.transverse_graph(self.mg.graph, start, directed=0):
if len(self.levels) == 0:
self.levels[n.index] = 1
else:
c = n.connections[0]
parent = c.partner(n.index)
self.levels[n.index] = self.levels[parent.index] + 1
self.nodes.append(n)
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 GraphNode of parent
:type parent: GraphNode
: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.MotifGraphException(
"cannot supply parent_end_index and parent_end_name together")
elif parent_end_name is not None:
parent_ends = parent.data.get_basepair(name=parent_end_name)
if len(parent_ends) == 0:
raise exceptions.MotifGraphException(
"cannot find parent_end_name: " + parent_end_name + " in "
"parent motif: " + parent.data.name)
if len(parent_ends) > 1:
raise exceptions.MotifGraphException(
"more then one end was found with parent_end_name: " +
parent_end_name + " in parent motif: " + parent.data.name)
parent_end = parent_ends[0]
parent_end_index = parent.data.ends.index(parent_end)
if parent_end_index == parent.data.block_end_add:
raise exceptions.MotifGraphException(
"cannot add motif: to graph as the parent_end_name" +
" supplied is blocked see class Motif")
available = parent.available_pos(parent_end_index)
if not available:
raise exceptions.MotifGraphException(
"cannot add motif to tree as the end " +
"you are trying to add it to is already filled or does "
"not exist")
return [parent_end_index]
elif parent_end_index != -1:
if parent_end_index == parent.data.block_end_add:
raise exceptions.MotifGraphException(
"cannot add motif: to tree as the parent_end_index" +
" supplied is blocked see class Motif")
available = parent.available_pos(parent_end_index)
if not available:
raise exceptions.MotifGraphException(
"cannot add motif to tree as the end " +
"you are trying to add it to is already filled or does "
"not exist")
return [parent_end_index]
else:
avail_pos = parent.available_children_pos()
final_avail_pos = []
for p in avail_pos:
if p == parent.data.block_end_add:
continue
final_avail_pos.append(p)
return final_avail_pos