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import gfapy
import unittest
class TestAPIReferencesEdgesGFA2(unittest.TestCase):
def test_edges_references(self):
g = gfapy.Gfa()
lab = gfapy.Line("E\t*\ta+\tb+\t0\t10\t90\t100$\t*")
self.assertEqual(gfapy.OrientedLine("a","+"), lab.sid1)
self.assertEqual(gfapy.OrientedLine("b","+"), lab.sid2)
sa = gfapy.Line("S\ta\t100\t*")
g.append(sa)
sb = gfapy.Line("S\tb\t100\t*")
g.append(sb)
g.append(lab)
self.assertEqual(sa, lab.sid1.line)
self.assertEqual(sb, lab.sid2.line)
lab.disconnect()
self.assertEqual("a", lab.sid1.line)
self.assertEqual("b", lab.sid2.line)
# disconnection of segment cascades on edges
g.append(lab)
assert(lab.is_connected())
self.assertEqual(sa, lab.sid1.line)
sa.disconnect()
assert(not lab.is_connected())
self.assertEqual("a", lab.sid1.line)
def test_edges_backreferences(self):
g = gfapy.Gfa()
sa = gfapy.Line("S\ta\t100\t*")
g.append(sa)
s = {}
for sbeg1, beg1 in {"0":0,"1":30,"2":70,"$":gfapy.LastPos("100$")}.items():
for send1, end1 in {"0":0,"1":30,"2":70,"$":gfapy.LastPos("100$")}.items():
if beg1 > end1:
continue
for sbeg2, beg2 in {"0":0,"1":30,"2":70,"$":gfapy.LastPos("100$")}.items():
for send2, end2 in {"0":0,"1":30,"2":70,"$":gfapy.LastPos("100$")}.items():
if beg2 > end2:
continue
for or1 in ["+","-"]:
for or2 in ["+","-"]:
eid = "<{}".format(or1)+"{}".format(or2)+"{}".format(sbeg1)+"{}".format(send1)+"{}".format(sbeg2)+"{}".format(send2)
other = "s{}".format(eid)
g.append("\t".join(["E",eid,"a{}".format(or1),"{}".format(other)+"{}".format(or2),
str(beg1),str(end1),str(beg2),str(end2),"*"]))
s[other] = gfapy.Line("S\t{}".format(other)+"\t100\t*")
g.append(s[other])
eid = ">{}".format(or1)+"{}".format(or2)+"{}".format(sbeg1)+"{}".format(send1)+"{}".format(sbeg2)+"{}".format(send2)
other = "s{}".format(eid)
g.append("\t".join(["E",eid,"{}".format(other)+"{}".format(or1),"a{}".format(or2),
str(beg1),str(end1),str(beg2),str(end2),"*"]))
s[other] = gfapy.Line("S\t{}".format(other)+"\t100\t*")
g.append(s[other])
exp_sa_d_L = []
exp_sa_d_R = []
exp_sa_e_cr = []
exp_sa_e_cd = []
exp_sa_i = []
# a from 0 to non-$, other from non-0 to $;
# same orientation;"d_L"
# opposite orientations;"internals"
for e_a in ["0","1","2"]:
for b_other in ["1","2","$"]:
for ors in ["++","--"]:
exp_sa_d_L.append("<{}".format(ors)+"0{}".format(e_a)+"{}".format(b_other)+"$")
exp_sa_d_L.append(">{}".format(ors)+"{}".format(b_other)+"$0{}".format(e_a))
for ors in ["+-","-+"]:
exp_sa_i.append("<{}".format(ors)+"0{}".format(e_a)+"{}".format(b_other)+"$")
exp_sa_i.append(">{}".format(ors)+"{}".format(b_other)+"$0{}".format(e_a))
# one from non-0 to non-$, other non-0 to non-$;"internals"
for pos_one in ["11","12","22"]:
for pos_other in ["11","12","22"]:
for ors in ["++","--","+-","-+"]:
for d in ["<",">"]:
exp_sa_i.append("{}".format(d)+"{}".format(ors)+"{}".format(pos_one)+"{}".format(pos_other))
# one from non-0 to non-$, other 0 to non-$;"internals"
for pos_one in ["11","12","22"]:
for pos_other in ["00","01","02"]:
for ors in ["++","--","+-","-+"]:
for d in ["<",">"]:
exp_sa_i.append("{}".format(d)+"{}".format(ors)+"{}".format(pos_one)+"{}".format(pos_other))
exp_sa_i.append("{}".format(d)+"{}".format(ors)+"{}".format(pos_other)+"{}".format(pos_one))
# one from non-0 to non-$, other non-0 to $;"internals"
for pos_one in ["11","12","22"]:
for pos_other in ["1$","2$","$$"]:
for ors in ["++","--","+-","-+"]:
for d in ["<",">"]:
exp_sa_i.append("{}".format(d)+"{}".format(ors)+"{}".format(pos_one)+"{}".format(pos_other))
exp_sa_i.append("{}".format(d)+"{}".format(ors)+"{}".format(pos_other)+"{}".format(pos_one))
# other from 0 to non-$, a from non-0 to $
# same orientation;"d_R"
# opposite orientations;"internals"
for e_other in ["0","1","2"]:
for b_a in ["1","2","$"]:
for ors in ["++","--"]:
exp_sa_d_R.append("<"+"{}".format(ors)+"{}".format(b_a)+"$0"+"{}".format(e_other))
exp_sa_d_R.append(">"+"{}".format(ors)+"0"+"{}".format(e_other)+"{}".format(b_a)+"$")
for ors in ["+-","-+"]:
exp_sa_i.append("<"+"{}".format(ors)+"{}".format(b_a)+"$0"+"{}".format(e_other))
exp_sa_i.append(">"+"{}".format(ors)+"0"+"{}".format(e_other)+"{}".format(b_a)+"$")
# both from 0 to non-$,
# opposite orientations;"d_L"
# same orientation;"internals"
for e1 in ["0","1","2"]:
for e2 in ["0","1","2"]:
pos = "0"+"{}".format(e1)+"0"+"{}".format(e2)
for ors in ["+-","-+"]:
for d in ["<",">"]:
exp_sa_d_L.append("{}".format(d)+"{}".format(ors)+"{}".format(pos))
for ors in ["++","--"]:
for d in ["<",">"]:
exp_sa_i.append("{}".format(d)+"{}".format(ors)+"{}".format(pos))
# both from non-0 to $,
# opposite orientations;"d_R"
# same orientation;"internals"
for e1 in ["1","2","$"]:
for e2 in ["1","2","$"]:
pos = "{}".format(e1)+"$"+"{}".format(e2)+"$"
for ors in ["+-","-+"]:
for d in ["<",">"]:
exp_sa_d_R.append("{}".format(d)+"{}".format(ors)+"{}".format(pos))
for ors in ["++","--"]:
for d in ["<",">"]:
exp_sa_i.append("{}".format(d)+"{}".format(ors)+"{}".format(pos))
# a whole; other non-whole:edges_to_containers
for pos_other in ["00","01","02","11","12","1$","22","2$","$$"]:
for ors in ["++","--","+-","-+"]:
exp_sa_e_cr.append("<{}".format(ors)+"0${}".format(pos_other))
exp_sa_e_cr.append(">{}".format(ors)+"{}".format(pos_other)+"0$")
# a not-whole; other whole:edges_to_contained
for pos_a in ["00","01","02","11","12","1$","22","2$","$$"]:
for ors in ["++","--","+-","-+"]:
exp_sa_e_cd.append("<{}".format(ors)+"{}".format(pos_a)+"0$")
exp_sa_e_cd.append(">{}".format(ors)+"0${}".format(pos_a))
# a sid1; both whole:edges_to_contained
for ors in ["++","--","+-","-+"]:
exp_sa_e_cd.append("<{}".format(ors)+"0$0$")
# a sid2; both whole:edges_to_containers
for ors in ["++","--","+-","-+"]:
exp_sa_e_cr.append(">{}".format(ors)+"0$0$")
# dovetails_[LR]
self.assertEqual(set(exp_sa_d_L), set([x.name for x in sa.dovetails_L]))
self.assertEqual(set(exp_sa_d_R), set([x.name for x in sa.dovetails_R]))
# dovetails()
self.assertEqual(sa.dovetails_L, sa.dovetails_of_end("L"))
self.assertEqual(sa.dovetails_R, sa.dovetails_of_end("R"))
self.assertEqual((sa.dovetails_L + sa.dovetails_R), sa.dovetails)
# neighbours
self.assertEqual(set(["s"+x for x in (exp_sa_d_L+exp_sa_d_R)]),
set([x.name for x in sa.neighbours]))
# edges_to_containers/contained
self.assertEqual(set(exp_sa_e_cr),
set([x.name for x in sa.edges_to_containers]))
self.assertEqual(set(exp_sa_e_cd),
set([x.name for x in sa.edges_to_contained]))
# containments
self.assertEqual(set(exp_sa_e_cr+exp_sa_e_cd),
set([x.name for x in sa.containments]))
# contained/containers
self.assertEqual(set(["s"+x for x in exp_sa_e_cr]),
set([x.name for x in sa.containers]))
self.assertEqual(set(["s"+x for x in exp_sa_e_cd]),
set([x.name for x in sa.contained]))
# internals
self.assertEqual(set(exp_sa_i), set([x.name for x in sa.internals]))
# upon disconnection
sa.disconnect()
self.assertEqual([], sa.dovetails_L)
self.assertEqual([], sa.dovetails_R)
self.assertEqual([], sa.dovetails_of_end("L"))
self.assertEqual([], sa.dovetails_of_end("R"))
self.assertEqual([], sa.neighbours)
self.assertEqual([], sa.edges_to_containers)
self.assertEqual([], sa.edges_to_contained)
self.assertEqual([], sa.containments)
self.assertEqual([], sa.contained)
self.assertEqual([], sa.containers)
self.assertEqual([], sa.internals)
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