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import gfapy
import unittest
class TestLineLink(unittest.TestCase):
def test_from_string(self):
fields=["L","1","+","2","-","12M","RC:i:1232","NM:i:3","ab:Z:abcd",
"FC:i:2321","KC:i:1212","MQ:i:40"]
string = "\t".join(fields)
gfapy.Line(string)
self.assertIsInstance(gfapy.Line(string), gfapy.line.edge.Link)
self.assertEqual(str(fields[0]), gfapy.Line(string).record_type)
self.assertEqual(str(fields[1]), gfapy.Line(string).from_segment)
self.assertEqual(str(fields[2]), gfapy.Line(string).from_orient)
self.assertEqual(str(fields[3]), gfapy.Line(string).to_segment)
self.assertEqual(str(fields[4]), gfapy.Line(string).to_orient)
self.assertEqual([gfapy.alignment.CIGAR.Operation(12, "M")],
gfapy.Line(string).overlap)
self.assertEqual(1232, gfapy.Line(string).RC)
self.assertEqual(3, gfapy.Line(string).NM)
self.assertEqual(2321, gfapy.Line(string).FC)
self.assertEqual(1212, gfapy.Line(string).KC)
self.assertEqual(40, gfapy.Line(string).MQ)
self.assertEqual("abcd", gfapy.Line(string).ab)
with self.assertRaises(gfapy.FormatError):
gfapy.Line((string+"\tH1"))
with self.assertRaises(gfapy.FormatError):
gfapy.Line("L\tH")
with self.assertRaises(gfapy.FormatError):
f=fields[:]
f[2]="x"
gfapy.Line("\t".join(f), vlevel = 2)
with self.assertRaises(gfapy.FormatError):
f=fields[:]
f[4]="x"
gfapy.Line("\t".join(f), vlevel = 2)
with self.assertRaises(gfapy.FormatError):
f=fields[:]
f[5]="x"
gfapy.Line("\t".join(f), vlevel = 2)
with self.assertRaises(gfapy.TypeError):
f=fields[:]
f[6]="RC:Z:1232"
gfapy.Line("\t".join(f), vlevel = 2)
with self.assertRaises(gfapy.TypeError):
f=fields[:]
f[7]="NM:Z:1232"
gfapy.Line("\t".join(f), vlevel = 2)
#TODO
#def test_coords
# g = RGFA.new(version: :gfa1)
# g << "S\t1\t*\tLN:i:100"
# g << "L\t1\t+\t2\t-\t1M2D10M1I"
# assert_equal([87,100], g.links[0].from_coords)
# assert_raises(RGFA::ValueError) {g.links[0].to_coords}
# g << "S\t2\t*\tLN:i:100"
# assert_equal([88,100], g.links[0].to_coords)
# g << "L\t3\t-\t4\t+\t10M2P3D1M"
# assert_equal([0,14], g.links[1].from_coords)
# assert_equal([0,11], g.links[1].to_coords)
#end
#def test_to_gfa2
# g = RGFA.new(version: :gfa1)
# g << "S\t1\t*\tLN:i:100"
# g << "S\t2\t*\tLN:i:100"
# g << "S\t3\t*\tLN:i:100"
# g << "S\t4\t*\tLN:i:100"
# g << "L\t1\t+\t2\t+\t10M"
# g << "L\t1\t-\t2\t-\t20M"
# g << "L\t3\t-\t4\t+\t30M"
# g << "L\t3\t+\t4\t-\t40M"
# assert_equal("E * 1+ 2+ 90 100$ 0 10 10M",
# g.links[0].to_gfa2_s)
# assert_equal("E * 1- 2- 0 20 80 100$ 20M",
# g.links[1].to_gfa2_s)
# assert_equal("E * 3- 4+ 0 30 0 30 30M",
# g.links[2].to_gfa2_s)
# assert_equal("E * 3+ 4- 60 100$ 60 100$ 40M",
# g.links[3].to_gfa2_s)
# assert_equal(RGFA::Line::Edge::Link, g.links[0].to_gfa1.class)
# assert_equal(RGFA::Line::Edge::GFA2, g.links[0].to_gfa2.class)
#end
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