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import gfapy
import unittest
class TestAPIReferencesGroups(unittest.TestCase):
def test_paths_references(self):
g = gfapy.Gfa()
s = {}; l = {}
for name in ["a", "b", "c", "d", "e", "f"]:
s[name] = gfapy.Line("S\t{}\t*".format(name))
g.append(s[name])
path = gfapy.Line("P\tp1\tf+,a+,b+,c-,e+\t*")
self.assertEqual([gfapy.OrientedLine("f","+"), gfapy.OrientedLine("a","+"),
gfapy.OrientedLine("b","+"), gfapy.OrientedLine("c","-"),
gfapy.OrientedLine("e","+")], path.segment_names)
self.assertEqual([], path.links)
# connection
g.append(path)
# add links
for name in ["a+b+", "b+c-", "c-d+", "e-c+", "a-f-"]:
l[name] = gfapy.Line("\t".join((list("L{}*".format(name)))))
g.append(l[name])
# segment_names
self.assertEqual([gfapy.OrientedLine(s["f"],"+"),
gfapy.OrientedLine(s["a"],"+"),
gfapy.OrientedLine(s["b"],"+"),
gfapy.OrientedLine(s["c"],"-"),
gfapy.OrientedLine(s["e"],"+")], path.segment_names)
# links
self.assertEqual([gfapy.OrientedLine(l["a-f-"],"-"),
gfapy.OrientedLine(l["a+b+"],"+"),
gfapy.OrientedLine(l["b+c-"],"+"),
gfapy.OrientedLine(l["e-c+"],"-")],
path.links)
# path disconnection
path.disconnect()
self.assertEqual([gfapy.OrientedLine("f","+"),
gfapy.OrientedLine("a","+"),
gfapy.OrientedLine("b","+"),
gfapy.OrientedLine("c","-"),
gfapy.OrientedLine("e","+")], path.segment_names)
self.assertEqual([], path.links)
g.append(path)
# links disconnection cascades on paths:
assert(path.is_connected())
l["a-f-"].disconnect()
assert(not path.is_connected())
self.assertEqual([gfapy.OrientedLine("f","+"),
gfapy.OrientedLine("a","+"),
gfapy.OrientedLine("b","+"),
gfapy.OrientedLine("c","-"),
gfapy.OrientedLine("e","+")], path.segment_names)
g.append(path)
g.append(l["a-f-"])
# segment disconnection cascades on links and then paths:
assert(path.is_connected())
s["a"].disconnect()
assert(not path.is_connected())
self.assertEqual([gfapy.OrientedLine("f","+"),
gfapy.OrientedLine("a","+"),
gfapy.OrientedLine("b","+"),
gfapy.OrientedLine("c","-"),
gfapy.OrientedLine("e","+")], path.segment_names)
self.assertEqual([], path.links)
def test_paths_backreferences(self):
g = gfapy.Gfa()
s = {}; l = {}
for name in ["a", "b", "c", "d", "e", "f"]:
s[name] = gfapy.Line("S\t{}\t*".format(name))
g.append(s[name])
path = gfapy.Line("P\tp1\tf+,a+,b+,c-,e+\t*")
g.append(path)
for sname in ["a", "b", "c", "e", "f"]:
self.assertEqual([path], s[sname].paths)
self.assertEqual([], s["d"].paths)
for name in ["a+b+", "b+c-", "c-d+", "e-c+", "a-f-"]:
l[name] = gfapy.Line("\t".join(list("L{}*".format(name))))
g.append(l[name])
for lname in ["a+b+", "b+c-", "e-c+", "a-f-"]:
self.assertEqual([path], l[lname].paths)
self.assertEqual([], l["c-d+"].paths)
# disconnection effects
path.disconnect()
for lname in ["a+b+", "b+c-", "c-d+", "e-c+", "a-f-"]:
self.assertEqual([], l[lname].paths)
for sname in ["a", "b", "c", "d", "e", "f"]:
self.assertEqual([], s[sname].paths)
# reconnection
path.connect(g)
for sname in ["a", "b", "c", "e", "f"]:
self.assertEqual([path], s[sname].paths)
self.assertEqual([], s["d"].paths)
for lname in ["a+b+", "b+c-", "e-c+", "a-f-"]:
self.assertEqual([path], l[lname].paths)
self.assertEqual([], l["c-d+"].paths)
def test_gfa2_paths_references(self):
g = gfapy.Gfa()
s = {}
for name in ["a", "b", "c", "d", "e", "f"]:
s[name] = gfapy.Line("S\t{}\t1000\t*".format(name))
g.append(s[name])
path1_part1 = gfapy.Line("O\tp1\tp2- b+")
path1_part2 = gfapy.Line("O\tp1\tc- e-c+-")
path1 = path1_part2
path2 = gfapy.Line("O\tp2\tf+ a+")
self.assertEqual([gfapy.OrientedLine("p2","-"),
gfapy.OrientedLine("b","+")], path1_part1.items)
self.assertEqual([gfapy.OrientedLine("c","-"),
gfapy.OrientedLine("e-c+","-")], path1_part2.items)
self.assertEqual([gfapy.OrientedLine("f","+"),
gfapy.OrientedLine("a","+")], path2.items)
with self.assertRaises(gfapy.RuntimeError): path1.captured_path
with self.assertRaises(gfapy.RuntimeError): path2.captured_path
# connection
g.append(path1_part1)
g.append(path1_part2)
g.append(path2)
# edges
e = {}
for name in ["a+b+", "b+c-", "c-d+", "e-c+", "a-f-", "f-b+"]:
coord1 = "900\t1000$" if (name[1] == "+") else "0\t100"
coord2 = "0\t100" if (name[3] == "+") else "900\t1000$"
e[name] = gfapy.Line("E\t{}\t{}\t{}\t{}\t{}\t100M".format(name,name[0:2],name[2:4],coord1,coord2))
g.append(e[name])
# items
self.assertEqual([gfapy.OrientedLine(path2,"-"),
gfapy.OrientedLine(s["b"],"+"),
gfapy.OrientedLine(s["c"],"-"),
gfapy.OrientedLine(e["e-c+"],"-")],
path1.items)
self.assertEqual([gfapy.OrientedLine(s["f"],"+"),
gfapy.OrientedLine(s["a"],"+")],
path2.items)
# induced set
self.assertEqual([gfapy.OrientedLine(s["f"],"+"),
gfapy.OrientedLine(e["a-f-"],"-"),
gfapy.OrientedLine(s["a"],"+")],
path2.captured_path)
self.assertEqual([gfapy.OrientedLine(s["a"],"-"),
gfapy.OrientedLine(e["a-f-"],"+"),
gfapy.OrientedLine(s["f"],"-"),
gfapy.OrientedLine(e["f-b+"],"+"),
gfapy.OrientedLine(s["b"],"+"),
gfapy.OrientedLine(e["b+c-"],"+"),
gfapy.OrientedLine(s["c"],"-"),
gfapy.OrientedLine(e["e-c+"],"-"),
gfapy.OrientedLine(s["e"],"+")],
path1.captured_path)
# backreferences
for line in [path2, s["b"], s["c"], e["e-c+"]]:
self.assertEqual([path1], line.paths)
for line in [s["f"], s["a"]]:
self.assertEqual([path2], line.paths)
# group disconnection
path1.disconnect()
self.assertEqual([gfapy.OrientedLine("p2","-"), gfapy.OrientedLine("b","+"), gfapy.OrientedLine("c","-"), gfapy.OrientedLine("e-c+","-")],
path1.items)
with self.assertRaises(gfapy.RuntimeError):
path1.captured_path
self.assertEqual([gfapy.OrientedLine(s["f"],"+"), gfapy.OrientedLine(s["a"],"+")], path2.items)
for line in [path2, s["b"], s["c"], e["e-c+"]]:
self.assertEqual([], line.paths)
# group reconnection
g.append(path1)
self.assertEqual([gfapy.OrientedLine(path2,"-"), gfapy.OrientedLine(s["b"],"+"), gfapy.OrientedLine(s["c"],"-"), gfapy.OrientedLine(e["e-c+"],"-")],
path1.items)
self.assertEqual([gfapy.OrientedLine(s["f"],"+"), gfapy.OrientedLine(s["a"],"+")], path2.items)
for line in [path2, s["b"], s["c"], e["e-c+"]]:
self.assertEqual([path1], line.paths)
# item disconnection cascades on group
assert(path1.is_connected())
assert(path2.is_connected())
e["e-c+"].disconnect()
assert(not path1.is_connected())
assert(path2.is_connected())
g.append(e["e-c+"])
g.append(path1)
# two-level disconnection cascade
assert(path1.is_connected())
assert(path2.is_connected())
s["f"].disconnect()
assert(not path2.is_connected())
assert(not path1.is_connected())
def test_sets_references(self):
g = gfapy.Gfa()
s = {}
set1 = gfapy.Line("U\tset1\tb set2 c e-c+")
set2 = gfapy.Line("U\tset2\tg c-d+ path1")
path1 = gfapy.Line("O\tpath1\tf+ a+")
self.assertEqual(["b", "set2", "c", "e-c+"], set1.items)
self.assertEqual(["g", "c-d+", "path1"], set2.items)
# induced set of non-connected cannot be computed
with self.assertRaises(gfapy.RuntimeError): set1.induced_set
with self.assertRaises(gfapy.RuntimeError): set2.induced_set
# connection
g.append(set1)
g.append(set2)
# induced set cannot be computed, as long as not all references are solved
with self.assertRaises(gfapy.RuntimeError): set1.induced_set
# connect items
g.append(path1)
for name in ["a", "b", "c", "d", "e", "f", "g"]:
s[name] = gfapy.Line("S\t"+"{}".format(name)+"\t1000\t*")
g.append(s[name])
e = {}
for name in ["a+b+", "b+c-", "c-d+", "e-c+", "a-f-"]:
coord1 = "900\t1000$" if (name[1] == "+") else "0\t100"
coord2 = "0\t100" if (name[3] == "+") else "900\t1000$"
e[name] = gfapy.Line("E\t{}\t{}\t{}\t{}\t{}\t100M".format(name,name[0:2],name[2:4],coord1,coord2))
g.append(e[name])
# items
self.assertEqual([s["b"], set2, s["c"], e["e-c+"]], set1.items)
self.assertEqual([s["g"], e["c-d+"], path1], set2.items)
# induced set
self.assertEqual([gfapy.OrientedLine(s["f"],"+"), gfapy.OrientedLine(s["a"],"+")],
path1.captured_segments)
self.assertEqual(set([x.name for x in [s["g"], s["c"], s["d"], s["f"], s["a"]]]),
set([x.name for x in set2.induced_segments_set]))
self.assertEqual(set([x.name for x in [s["b"], s["g"], s["c"], s["d"], s["f"], s["a"], s["e"]]]),
set([x.name for x in set1.induced_segments_set]))
self.assertEqual(set([x.name for x in [e["c-d+"], e["a-f-"]]]),
set([x.name for x in set2.induced_edges_set]))
self.assertEqual([e["a+b+"],e["b+c-"],e["c-d+"],e["e-c+"],e["a-f-"]],
set1.induced_edges_set)
self.assertEqual(set([x.name for x in set1.induced_segments_set + set1.induced_edges_set]),
set([x.name for x in set1.induced_set]))
# backreferences
for line in [s["b"], set2, s["c"], e["e-c+"]]:
self.assertEqual([set1], line.sets)
for line in [s["g"], e["c-d+"], path1]:
self.assertEqual([set2], line.sets)
# group disconnection
set1.disconnect()
self.assertEqual(["b", "set2", "c", "e-c+"], set1.items)
for line in [s["b"], set2, s["c"], e["e-c+"]]:
self.assertEqual([], line.sets)
# group reconnection
g.append(set1)
self.assertEqual([s["b"], set2, s["c"], e["e-c+"]], set1.items)
for line in [s["b"], set2, s["c"], e["e-c+"]]:
self.assertEqual([set1], line.sets)
# item disconnection cascades on group
assert(set1.is_connected())
e["e-c+"].disconnect()
assert(not set1.is_connected())
g.append(e["e-c+"])
g.append(set1)
# multilevel disconnection cascade
assert(path1.is_connected())
assert(set2.is_connected())
assert(set1.is_connected())
s["f"].disconnect()
assert(not path1.is_connected())
assert(not set2.is_connected())
assert(not set1.is_connected())
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