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import gfapy
import unittest
class TestAPILinesDestructors(unittest.TestCase):
def test_delete_links(self):
gfa = gfapy.Gfa()
s = ["S\t0\t*", "S\t1\t*", "S\t2\t*"]
l = "L\t1\t+\t2\t+\t12M"
c = "C\t1\t+\t0\t+\t12\t12M"
for line in (s + [l,c]): gfa.append(line)
self.assertEqual([l], [str(x) for x in gfa.dovetails])
self.assertEqual([l], [str(x) for x in \
gfa.segment("1").end_relations("R", ["2", "L"])])
for x in gfa.segment("1").oriented_relations("+", \
gfapy.OrientedLine("2", "+")):
x.disconnect()
self.assertEqual([], gfa.dovetails)
self.assertEqual([], gfa.segment("1").end_relations("R", ["2", "L"]))
self.assertEqual([c], [str(x) for x in gfa.containments])
self.assertEqual(c,
str(gfa.segment("1").relations_to(gfa.segment("0"),
"edges_to_contained")[0]))
gfa.append(l)
self.assertNotEqual([], gfa.dovetails)
for x in gfa.segment("1").oriented_relations("+", \
gfapy.OrientedLine("2", "+")):
x.disconnect()
self.assertEqual([], gfa.dovetails)
def test_delete_containments(self):
gfa = gfapy.Gfa()
s = ["S\t0\t*", "S\t1\t*", "S\t2\t*"]
l = "L\t1\t+\t2\t+\t12M"
c = "C\t1\t+\t0\t+\t12\t12M"
for line in (s + [l,c]): gfa.append(line)
for x in gfa.segment("1").relations_to(gfa.segment("0"), "edges_to_contained"):
x.disconnect()
self.assertEqual([], gfa.containments)
self.assertEqual(0, len(gfa.segment("1").relations_to("0",
"edges_to_contained")))
gfa.append(c)
self.assertNotEqual([], gfa.containments)
self.assertEqual(c, str(gfa.segment("1").relations_to("0",
"edges_to_contained")[0]))
for x in gfa.segment("1").relations_to(gfa.segment("0"), "edges_to_contained"):
x.disconnect()
self.assertEqual([], gfa.containments)
def test_delete_segment(self):
gfa = gfapy.Gfa()
gfa.append("H\tVN:Z:1.0")
s = ["S\t0\t*", "S\t1\t*", "S\t2\t*"]
l = "L\t1\t+\t2\t+\t12M"
c = "C\t1\t+\t0\t+\t12\t12M"
p = "P\t4\t2+,0-\t12M"
for line in (s + [l,c,p]): gfa.append(line)
self.assertEqual(set(s), set([str(x) for x in gfa.segments]))
self.assertEqual(set(["0", "1", "2"]), set(gfa.segment_names))
self.assertEqual([l], [str(x) for x in gfa.dovetails if not x.virtual])
self.assertEqual([c], [str(x) for x in gfa.containments])
self.assertEqual([p], [str(x) for x in gfa.paths])
self.assertEqual(["4"], gfa.path_names)
gfa.segment("0").disconnect()
self.assertEqual(set([s[1],s[2]]), set([str(x) for x in gfa.segments]))
self.assertEqual(set(["1", "2"]), set(gfa.segment_names))
self.assertEqual([l], [str(x) for x in gfa.dovetails if not x.virtual])
self.assertEqual([], [str(x) for x in gfa.containments])
self.assertEqual([], [str(x) for x in gfa.paths])
self.assertEqual([], gfa.path_names)
gfa.segment("1").disconnect()
self.assertEqual([s[2]], [str(x) for x in gfa.segments])
self.assertEqual([], gfa.dovetails)
gfa.rm("2")
self.assertEqual([], gfa.segments)
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