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import gfapy
import unittest
class TestAPIReferencesVirtual(unittest.TestCase):
def test_edges_gaps_create_virtual_segments(self):
data = [
["gfa1", {"lines":["L\ta\t+\tb\t-\t*", "C\ta\t-\tb\t+\t100\t*"],
"m1":"oriented_from", "m2":"oriented_to",
"sA":"S\ta\t*", "sB":"S\tb\t*",
"collection":"edges"}],
["gfa2", {"lines":["E\t*\ta+\tb-\t0\t100\t900\t1000$\t*"],
"m1":"sid1", "m2":"sid2",
"sA":"S\ta\t1000\t*", "sB":"S\tb\t1000\t*",
"collection":"edges"}],
["gfa2", {"lines":["G\t*\ta+\tb-\t1000\t100"],
"m1":"sid1", "m2":"sid2",
"sA":"S\ta\t1000\t*", "sB":"S\tb\t1000\t*",
"collection":"gaps"}]
]
for v,values in data:
for linestr in values["lines"]:
g = gfapy.Gfa(version=v)
line = gfapy.Line(linestr)
g.append(line)
self.assertEqual(set(["a", "b"]), set([x.name for x in g.segments]))
for s in g.segments: assert(s.virtual)
sA = gfapy.Line(values["sA"])
g.append(sA)
self.assertEqual(set(["a", "b"]), set([x.name for x in g.segments]))
assert(not g.segment("a").virtual)
assert(g.segment("b").virtual)
self.assertEqual(sA, getattr(line,values["m1"]).line)
self.assertEqual(sA, g.segment("a"))
self.assertEqual([line], getattr(sA,values["collection"]))
sB = gfapy.Line(values["sB"])
g.append(sB)
self.assertEqual(set(["a", "b"]), set([x.name for x in g.segments]))
assert(not g.segment("b").virtual)
self.assertEqual(sB, getattr(line,values["m2"]).line)
self.assertEqual(sB, g.segment("b"))
self.assertEqual([line], getattr(sB,values["collection"]))
def test_fragments_create_virtual_segments(self):
g = gfapy.Gfa(version="gfa2")
fr = gfapy.Line("F\ta\tread10-\t0\t10\t990\t1000$\t*")
g.append(fr)
self.assertEqual(["a"], [x.name for x in g.segments])
assert(g.segment("a").virtual)
sA = gfapy.Line("S\ta\t1000\t*")
g.append(sA)
self.assertEqual(["a"], [x.name for x in g.segments])
assert(not g.segment("a").virtual)
self.assertEqual(sA, fr.sid)
self.assertEqual(sA, g.segment("a"))
self.assertEqual([fr], sA.fragments)
def test_paths_create_virtual_links(self):
g = gfapy.Gfa(version="gfa1")
path = gfapy.Line("P\tp1\tb+,ccc-,e+\t10M1I2M,15M")
g.append(path)
for i in path.segment_names: assert(i.line.virtual)
self.assertEqual(set(["b", "ccc", "e"]), set([x.name for x in g.segments]))
sB = gfapy.Line("S\tb\t*")
g.append(sB)
assert(not path.segment_names[0].line.virtual)
self.assertEqual(sB, path.segment_names[0].line)
self.assertEqual([path], sB.paths)
for i in path.links: assert(i.line.virtual)
l = gfapy.Line("L\tccc\t+\tb\t-\t2M1D10M")
g.append(l)
assert(not path.links[0].line.virtual)
self.assertEqual(l, path.links[0].line)
self.assertEqual([path], l.paths)
l = gfapy.Line("L\tccc\t-\te\t+\t15M")
g.append(l)
assert(not path.links[1].line.virtual)
self.assertEqual(l, path.links[1].line)
self.assertEqual([path], l.paths)
def test_ordered_groups_create_virtual_unknown_records(self):
g = gfapy.Gfa(version="gfa2")
path = gfapy.Line("O\tp1\tchildpath- b+ c- edge-")
g.append(path)
for i in path.items:
assert(i.line.virtual)
self.assertEqual("\n", i.line.record_type)
childpath = gfapy.Line("O\tchildpath\tf+ a+")
g.append(childpath)
assert(not path.items[0].line.virtual)
self.assertEqual(childpath, path.items[0].line)
self.assertEqual([path], childpath.paths)
sB = gfapy.Line("S\tb\t1000\t*")
g.append(sB)
assert(not path.items[1].line.virtual)
self.assertEqual(sB, path.items[1].line)
self.assertEqual([path], sB.paths)
edge = gfapy.Line("E\tedge\te-\tc+\t0\t100\t900\t1000$\t*")
g.append(edge)
assert(not path.items[-1].line.virtual)
self.assertEqual(edge, path.items[-1].line)
self.assertEqual([path], edge.paths)
def test_unordered_groups_create_virtual_unknown_records(self):
g = gfapy.Gfa(version="gfa2")
set = gfapy.Line("U\tset\tchildpath b childset edge")
g.append(set)
for i in set.items:
assert(i.virtual)
self.assertEqual("\n", i.record_type)
childpath = gfapy.Line("O\tchildpath\tf+ a+")
g.append(childpath)
assert(not set.items[0].virtual)
self.assertEqual(childpath, set.items[0])
self.assertEqual([set], childpath.sets)
sB = gfapy.Line("S\tb\t1000\t*")
g.append(sB)
assert(not set.items[1].virtual)
self.assertEqual(sB, set.items[1])
self.assertEqual([set], sB.sets)
childset = gfapy.Line("U\tchildset\tg edge2")
g.append(childset)
assert(not set.items[2].virtual)
self.assertEqual(childset, set.items[2])
self.assertEqual([set], childset.sets)
edge = gfapy.Line("E\tedge\te-\tc+\t0\t100\t900\t1000$\t*")
g.append(edge)
assert(not set.items[3].virtual)
self.assertEqual(edge, set.items[3])
self.assertEqual([set], edge.sets)
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