def __get_prd_for_scaffold(self, prd_file_name):
for e1id, e2id, D, weight, delta in saveparser.prd(prd_file_name):
if (e1id, e2id) not in self.prd:
e1 = self.graph.es[e1id]
e2 = self.graph.es[e2id]
if len(e1.v2.out) != 0 or len(e2.v1.inn) != 0:
continue
if D - e1.len > 0 and D - e1.len < self.d:
if (e1id, e2id) not in self.prd_for_scaffold:
self.prd_for_scaffold[(e1id, e2id)] = []
self.prd_for_scaffold[(e1id, e2id)].append((D, weight, delta))
def __get_additional_prd(self, prd_file_name):
for e1id, e2id, D, weight, delta in saveparser.prd(prd_file_name):
if (e1id, e2id) not in self.prd:
e1= self.graph.es[e1id]
e2 = self.graph.es[e2id]
if len(e1.v2.out) != 0 or len(e2.v1.inn) != 0:
continue
e1_len = e1.len
if D - e1_len > 0 and D - e1_len < 100:
if (e1id, e2id) not in self.additional_prd:
self.additional_prd[(e1id, e2id)] = []
self.additional_prd[(e1id, e2id)].append((D, weight, delta))
def __get_prd_for_scaffold(self, prd_file_name):
for e1id, e2id, D, weight, delta in saveparser.prd(prd_file_name):
if (e1id, e2id) not in self.prd:
e1 = self.graph.es[e1id]
e2 = self.graph.es[e2id]
if len(e1.v2.out) != 0 or len(e2.v1.inn) != 0:
continue
if D - e1.len > 0 and D - e1.len < self.d:
if (e1id, e2id) not in self.prd_for_scaffold:
self.prd_for_scaffold[(e1id, e2id)] = []
self.prd_for_scaffold[(e1id, e2id)].append(
(D, weight, delta))
def __use_prd(self, prd_filename, config):
for e1id, e2id, D, weight, delta in saveparser.prd(prd_filename):
e1 = self.graph.es[e1id]
e2 = self.graph.es[e2id]
if (e1, e2) not in self.rectangles: # there' no possible rectangles between e1 and e2
continue
r = self.rectangles[(e1, e2)]
for diag in r.diagonals.itervalues():
diag.inc_prd_support(D, weight, delta, config)
if diag != diag.conj:
diag.conj.inc_prd_support(
D - e1.len + e2.len, weight, delta, config
) # TODO: check if prd is symmetric or not
def __use_prd(self, prd_filename, config):
for e1id, e2id, D, weight, delta in saveparser.prd(prd_filename):
e1 = self.graph.es[e1id]
e2 = self.graph.es[e2id]
if (
e1, e2
) not in self.rectangles: # there' no possible rectangles between e1 and e2
continue
r = self.rectangles[(e1, e2)]
for diag in r.diagonals.itervalues():
diag.inc_prd_support(D, weight, delta, config)
if diag != diag.conj:
diag.conj.inc_prd_support(
D - e1.len + e2.len, weight, delta,
config) # TODO: check if prd is symmetric or not
def __get_prd(self, prd_file_name):
for e1id, e2id, D, weight, delta in saveparser.prd(prd_file_name):
self.prd[(e1id, e2id)] = (D, weight, delta + 2)
def __get_prd(self, prd_file_name):
for e1id, e2id, D, weight, delta in saveparser.prd(prd_file_name):
if (e1id, e2id) not in self.prd:
self.prd[(e1id, e2id)] = []
self.prd[(e1id, e2id)].append((D, weight, delta))
def __get_prd(self, prd_file_name):
for e1id, e2id, D, weight, delta in saveparser.prd(prd_file_name):
if (e1id, e2id) not in self.prd:
self.prd[(e1id, e2id)] = []
self.prd[(e1id, e2id)].append((D, weight, delta))
