def test_interc(c1,c2,join_options,graph,ends,linked):
os1=oscaffold[c1]
os1_mine = (args.fromS <= os1) and (os1 < args.endS)
if not os1_mine: return([-100])
# print "test interc",c1,c2,oscaffold[c1],oscaffold[c2],ends[oscaffold[c1]],ends[oscaffold[c2]],linked.get(c1),linked.get(c2),len(linked.keys())
if False:
for free_end in ends[scaffold[c1]]:
for c2_end in [c2+".5",c2+".3"]:
if c2_end in linked:
# print 1,free_end,c2_end
try:
gs.test_interc_option( c2_end, linked[c2_end], free_end, join_options, graph )
except Exception as e:
print("c2_end=",c2_end,"--",linked[c2_end],free_end)
print(e)
raise Exception('too connected 1')
for free_end in ends[scaffold[c2]]:
for c1_end in [c1+".5",c1+".3"]:
if c1_end in linked:
# print 2,free_end,c1_end
try:
gs.test_interc_option( c1_end, linked[c1_end], free_end, join_options, graph )
except Exception as e:
print("c1_end=",c1_end,"--",linked[c1_end],free_end)
print(e)
raise Exception('too connected 2')
if len(join_options)>0:
join_options.sort(reverse=True)
# print join_options
return(join_options[0])
return([-100.0])
def test_interc(c1, c2, join_options, graph, ends, linked):
os1 = oscaffold[c1]
os1_mine = (args.fromS <= os1) and (os1 < args.endS)
if not os1_mine: return ([-100])
# print "test interc",c1,c2,oscaffold[c1],oscaffold[c2],ends[oscaffold[c1]],ends[oscaffold[c2]],linked.get(c1),linked.get(c2),len(linked.keys())
if False:
for free_end in ends[scaffold[c1]]:
for c2_end in [c2 + ".5", c2 + ".3"]:
if c2_end in linked:
# print 1,free_end,c2_end
try:
gs.test_interc_option(c2_end, linked[c2_end], free_end,
join_options, graph)
except Exception as e:
print("c2_end=", c2_end, "--", linked[c2_end],
free_end)
print(e)
raise Exception('too connected 1')
for free_end in ends[scaffold[c2]]:
for c1_end in [c1 + ".5", c1 + ".3"]:
if c1_end in linked:
# print 2,free_end,c1_end
try:
gs.test_interc_option(c1_end, linked[c1_end], free_end,
join_options, graph)
except Exception as e:
print("c1_end=", c1_end, "--", linked[c1_end], free_end)
print(e)
raise Exception('too connected 2')
if len(join_options) > 0:
join_options.sort(reverse=True)
# print join_options
return (join_options[0])
return ([-100.0])
def test_interc(c1, c2, join_options, graph, ends, linked, slen,
max_interc_len):
os1 = oscaffold.get(c1, -1)
#os1_mine = (args.fromS <= os1) and (os1 < args.endS)
#if not os1_mine: return([-100])
#print "test interc:",c1,c2,oscaffold.get(c1,0),oscaffold.get(c2,0) ,ends[scaffold[c1]],ends[scaffold[c2]]#,c2_end in linked, c1_end in linked #,linked.get(c1),linked.get(c2),len(linked.keys())
print("test interc:", c1, c2, scaffold[c1], scaffold[c2],
ends[scaffold[c1]], ends[scaffold[c2]])
if slen[scaffold[c1]] < max_interc_len:
for free_end in ends[scaffold[c1]]:
for c2_end in [c2 + ".5", c2 + ".3"]:
# print "c2_end in linked:",c2_end,c2_end in linked
if c2_end in linked:
print(1, free_end, c2_end)
try:
gs.test_interc_option(c2_end, linked[c2_end], free_end,
join_options, graph)
except Exception as e:
print("c2_end=", c2_end, "--", linked[c2_end],
free_end)
print(e)
raise Exception('too connected 1')
if slen[scaffold[c2]] < max_interc_len:
for free_end in ends[scaffold[c2]]:
for c1_end in [c1 + ".5", c1 + ".3"]:
# print "c1_end in linked:",c1_end,c1_end in linked
if c1_end in linked:
print(2, free_end, c1_end)
try:
gs.test_interc_option(c1_end, linked[c1_end], free_end,
join_options, graph)
except Exception as e:
print("c1_end=", c1_end, "--", linked[c1_end],
free_end)
print(e)
raise Exception('too connected 2')
if len(join_options) > 0:
join_options.sort(reverse=True)
print("join options:", join_options)
return (join_options[0])
return ([-100.0])
def test_interc(c1,c2,join_options,graph,ends,linked,slen,max_interc_len):
os1=oscaffold.get(c1,-1)
#os1_mine = (args.fromS <= os1) and (os1 < args.endS)
#if not os1_mine: return([-100])
#print "test interc:",c1,c2,oscaffold.get(c1,0),oscaffold.get(c2,0) ,ends[scaffold[c1]],ends[scaffold[c2]]#,c2_end in linked, c1_end in linked #,linked.get(c1),linked.get(c2),len(linked.keys())
print("test interc:", c1,c2,scaffold[c1],scaffold[c2],ends[scaffold[c1]],ends[scaffold[c2]])
if slen[scaffold[c1]] < max_interc_len:
for free_end in ends[scaffold[c1]]:
for c2_end in [c2+".5",c2+".3"]:
# print "c2_end in linked:",c2_end,c2_end in linked
if c2_end in linked:
print(1,free_end,c2_end)
try:
gs.test_interc_option( c2_end, linked[c2_end], free_end, join_options, graph )
except Exception as e:
print("c2_end=",c2_end,"--",linked[c2_end],free_end)
print(e)
raise Exception('too connected 1')
if slen[scaffold[c2]] < max_interc_len:
for free_end in ends[scaffold[c2]]:
for c1_end in [c1+".5",c1+".3"]:
# print "c1_end in linked:",c1_end,c1_end in linked
if c1_end in linked:
print(2,free_end,c1_end)
try:
gs.test_interc_option( c1_end, linked[c1_end], free_end, join_options, graph )
except Exception as e:
print("c1_end=",c1_end,"--",linked[c1_end],free_end)
print(e)
raise Exception('too connected 2')
if len(join_options)>0:
join_options.sort(reverse=True)
print("join options:",join_options)
return(join_options[0])
return([-100.0])