def PreFilterEdges2(G, G_prime, Scaffolds, small_scaffolds, param):
#### Filter out edges that only has links far in on a contig (not near contig ends)####
pre_filtered = 0
for edge in G.edges():
if edge[0][0] != edge[1][0]:
node1 = edge[0][0]
node2 = edge[1][0]
side1 = edge[0][1]
side2 = edge[1][1]
n = G[edge[0]][edge[1]]['nr_links']
#calculate ML distance here
d = 1500
# Get the lower bound on each side here
if side1 == 'R':
try:
z_hat = Scaffolds[node1 ].lower_right_nbrs_obs[(node2, side2)]
except KeyError:
z_hat = small_scaffolds[node1 ].lower_right_nbrs_obs[(node2, side2)]
print z_hat, ((1 - normcdf(d + z_hat, param.mean_ins_size, param.std_dev_ins_size)) / (1 - normcdf(d + param.read_len, param.mean_ins_size, param.std_dev_ins_size))) ** n
else:
try:
z_hat = Scaffolds[node1 ].lower_left_nbrs_obs[(node2, side2)]
except KeyError:
z_hat = small_scaffolds[node1 ].lower_left_nbrs_obs[(node2, side2)]
print z_hat, ((1 - normcdf(d + z_hat, param.mean_ins_size, param.std_dev_ins_size)) / (1 - normcdf(d + param.read_len, param.mean_ins_size, param.std_dev_ins_size))) ** n
if side2 == 'R':
try:
z_hat2 = Scaffolds[node2 ].lower_right_nbrs_obs[(node1, side1)]
except KeyError:
z_hat2 = small_scaffolds[node2 ].lower_right_nbrs_obs[(node1, side1)]
print z_hat2, ((1 - normcdf(d + z_hat2, param.mean_ins_size, param.std_dev_ins_size)) / (1 - normcdf(d + param.read_len, param.mean_ins_size, param.std_dev_ins_size))) ** n
else:
try:
z_hat2 = Scaffolds[node2 ].lower_left_nbrs_obs[(node1, side1)]
except KeyError:
z_hat2 = small_scaffolds[node2 ].lower_left_nbrs_obs[(node1, side1)]
print z_hat2, ((1 - normcdf(d + z_hat2, param.mean_ins_size, param.std_dev_ins_size)) / (1 - normcdf(d + param.read_len, param.mean_ins_size, param.std_dev_ins_size))) ** n
print 'Nr of edges that did not pass the pre filtering step: ', pre_filtered
return()
def PreFilterEdges2(G, G_prime, Scaffolds, small_scaffolds, param):
#### Filter out edges that only has links far in on a contig (not near contig ends)####
pre_filtered = 0
for edge in G.edges():
if edge[0][0] != edge[1][0]:
node1 = edge[0][0]
node2 = edge[1][0]
side1 = edge[0][1]
side2 = edge[1][1]
n = G[edge[0]][edge[1]]['nr_links']
#calculate ML distance here
d = 1500
# Get the lower bound on each side here
if side1 == 'R':
try:
z_hat = Scaffolds[node1].lower_right_nbrs_obs[(node2,
side2)]
except KeyError:
z_hat = small_scaffolds[node1].lower_right_nbrs_obs[(
node2, side2)]
print z_hat, (
(1 - normcdf(d + z_hat, param.mean_ins_size,
param.std_dev_ins_size)) /
(1 - normcdf(d + param.read_len, param.mean_ins_size,
param.std_dev_ins_size)))**n
else:
try:
z_hat = Scaffolds[node1].lower_left_nbrs_obs[(node2,
side2)]
except KeyError:
z_hat = small_scaffolds[node1].lower_left_nbrs_obs[(node2,
side2)]
print z_hat, (
(1 - normcdf(d + z_hat, param.mean_ins_size,
param.std_dev_ins_size)) /
(1 - normcdf(d + param.read_len, param.mean_ins_size,
param.std_dev_ins_size)))**n
if side2 == 'R':
try:
z_hat2 = Scaffolds[node2].lower_right_nbrs_obs[(node1,
side1)]
except KeyError:
z_hat2 = small_scaffolds[node2].lower_right_nbrs_obs[(
node1, side1)]
print z_hat2, (
(1 - normcdf(d + z_hat2, param.mean_ins_size,
param.std_dev_ins_size)) /
(1 - normcdf(d + param.read_len, param.mean_ins_size,
param.std_dev_ins_size)))**n
else:
try:
z_hat2 = Scaffolds[node2].lower_left_nbrs_obs[(node1,
side1)]
except KeyError:
z_hat2 = small_scaffolds[node2].lower_left_nbrs_obs[(
node1, side1)]
print z_hat2, (
(1 - normcdf(d + z_hat2, param.mean_ins_size,
param.std_dev_ins_size)) /
(1 - normcdf(d + param.read_len, param.mean_ins_size,
param.std_dev_ins_size)))**n
print 'Nr of edges that did not pass the pre filtering step: ', pre_filtered
return ()
def Part(a, b):
expr1 = (min(len1, len2) - param.read_len) / k * normcdf(a, 0, 1)
expr2 = (b * std_dev) / k * (normcdf(b, 0, 1) - normcdf(a, 0, 1))
expr3 = (std_dev / k) * (normpdf(b, 0, 1) - normpdf(a, 0, 1))
value = expr1 + expr2 + expr3
return value
def Part(a, b):
expr1 = (min(len1, len2) - param.read_len) / k * normcdf(a, 0, 1)
expr2 = (b * std_dev) / k * (normcdf(b, 0, 1) - normcdf(a, 0, 1))
expr3 = (std_dev / k) * (normpdf(b, 0, 1) - normpdf(a, 0, 1))
value = expr1 + expr2 + expr3
return value