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import unittest
import gfapy
class TestUnitLineFinders(unittest.TestCase):
l_gfa1_str = ["S\t1\t*",
"S\t2\t*",
"S\t3\t*",
"S\t4\tCGAT",
"L\t1\t+\t2\t+\t*",
"L\t1\t-\t3\t+\t10M",
"C\t1\t-\t4\t-\t1\t*",
"P\tp1\t1+,2+\t*"]
l_gfa1 = [gfapy.Line(s) for s in l_gfa1_str]
gfa1 = gfapy.Gfa(l_gfa1)
l_gfa2_str = ["S\t5\t100\t*",
"S\t6\t110\t*",
"E\te1\t5+\t6-\t0\t100$\t10\t110$\t*",
"G\tg1\t5-\t6-\t1000\t*",
"O\to1\t5+ 6-",
"U\tu1\t5 e1",
"F\t5\tread1-\t0\t10\t102\t122\t*",
"F\t5\tread1-\t30\t100$\t180\t255\t*",
"F\t6\tread1-\t40\t50\t52\t64\t*",
"X\tx1\txx:Z:A",
"X\tx2",
"G\t*\t5+\t6+\t2000\t*"]
l_gfa2 = [gfapy.Line(s) for s in l_gfa2_str]
gfa2 = gfapy.Gfa(l_gfa2)
def test_search_link(self):
# search using the direct link
self.assertEqual(TestUnitLineFinders.l_gfa1[4], TestUnitLineFinders.gfa1._search_link(gfapy.OrientedLine("1","+"), gfapy.OrientedLine("2","+"), "*"))
# search using the complement link
self.assertEqual(TestUnitLineFinders.l_gfa1[4], TestUnitLineFinders.gfa1._search_link(gfapy.OrientedLine("2","-"), gfapy.OrientedLine("1","-"), "*"))
# with cigar parameter, but placeholder in line
self.assertEqual(TestUnitLineFinders.l_gfa1[4],
TestUnitLineFinders.gfa1._search_link(gfapy.OrientedLine("1","+"), gfapy.OrientedLine("2","+"), "10M"))
# with cigar parameter, and cigar in line
self.assertEqual(TestUnitLineFinders.l_gfa1[5],
TestUnitLineFinders.gfa1._search_link(gfapy.OrientedLine("1","-"), gfapy.OrientedLine("3","+"), "10M"))
self.assertEqual(None,
TestUnitLineFinders.gfa1._search_link(gfapy.OrientedLine("1","-"), gfapy.OrientedLine("3","+"), "12M"))
# with placeholder parameter, and cigar in line
self.assertEqual(TestUnitLineFinders.l_gfa1[5],
TestUnitLineFinders.gfa1._search_link(gfapy.OrientedLine("1","-"), gfapy.OrientedLine("3","+"), "*"))
def test_search_duplicate_gfa1(self):
# link
self.assertEqual(TestUnitLineFinders.l_gfa1[4], TestUnitLineFinders.gfa1._search_duplicate(TestUnitLineFinders.l_gfa1[4]))
# complement link
self.assertEqual(TestUnitLineFinders.l_gfa1[4], TestUnitLineFinders.gfa1._search_duplicate(TestUnitLineFinders.l_gfa1[4].complement()))
# containment
self.assertEqual(None, TestUnitLineFinders.gfa1._search_duplicate(TestUnitLineFinders.l_gfa1[6]))
# segment
self.assertEqual(TestUnitLineFinders.l_gfa1[0], TestUnitLineFinders.gfa1._search_duplicate(TestUnitLineFinders.l_gfa1[0]))
# path
self.assertEqual(TestUnitLineFinders.l_gfa1[7], TestUnitLineFinders.gfa1._search_duplicate(TestUnitLineFinders.l_gfa1[7]))
def test_search_duplicate_gfa2(self):
# line with mandatory name
self.assertEqual(TestUnitLineFinders.l_gfa2[0], TestUnitLineFinders.gfa2._search_duplicate(TestUnitLineFinders.l_gfa2[0]))
# line with optional name, present
self.assertEqual(TestUnitLineFinders.l_gfa2[2], TestUnitLineFinders.gfa2._search_duplicate(TestUnitLineFinders.l_gfa2[2]))
self.assertEqual(TestUnitLineFinders.l_gfa2[3], TestUnitLineFinders.gfa2._search_duplicate(TestUnitLineFinders.l_gfa2[3]))
self.assertEqual(TestUnitLineFinders.l_gfa2[4], TestUnitLineFinders.gfa2._search_duplicate(TestUnitLineFinders.l_gfa2[4]))
self.assertEqual(TestUnitLineFinders.l_gfa2[5], TestUnitLineFinders.gfa2._search_duplicate(TestUnitLineFinders.l_gfa2[5]))
# line with optional name, not present
self.assertEqual(None, TestUnitLineFinders.gfa2._search_duplicate(TestUnitLineFinders.l_gfa2[11]))
# line with no name
self.assertEqual(None, TestUnitLineFinders.gfa2._search_duplicate(TestUnitLineFinders.l_gfa2[6]))
self.assertEqual(None, TestUnitLineFinders.gfa2._search_duplicate(TestUnitLineFinders.l_gfa2[9]))
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