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import unittest
import gfapy
class TestLineContainment(unittest.TestCase):
def test_from_string(self):
fields = ["C","1","+","2","-","12","12M","MQ:i:1232","NM:i:3","ab:Z:abcd"]
string="\t".join(fields)
gfapy.Line(string)
self.assertIsInstance(gfapy.Line(string), gfapy.line.edge.Containment)
self.assertEqual(fields[0], gfapy.Line(string).record_type)
self.assertEqual(fields[1], gfapy.Line(string).from_segment)
self.assertEqual(fields[2], gfapy.Line(string).from_orient)
self.assertEqual(fields[3], gfapy.Line(string).to_segment)
self.assertEqual(fields[4], gfapy.Line(string).to_orient)
self.assertEqual(12, gfapy.Line(string).pos)
self.assertEqual([gfapy.alignment.cigar.CIGAR.Operation(12, "M")],
gfapy.Line(string).overlap)
self.assertEqual(1232, gfapy.Line(string).MQ)
self.assertEqual(3, gfapy.Line(string).NM)
self.assertEqual("abcd", gfapy.Line(string).ab)
with self.assertRaises(gfapy.FormatError):
gfapy.Line(string+"\tH1")
with self.assertRaises(gfapy.FormatError):
gfapy.Line(string+"\tH1")
with self.assertRaises(gfapy.FormatError):
gfapy.Line("C\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.FormatError):
f=fields[:]
f[6]="x"
gfapy.Line("\t".join(f), vlevel = 2)
with self.assertRaises(gfapy.TypeError):
f=fields[:]
f[7]="MQ:Z:1232"
gfapy.Line("\t".join(f), vlevel = 2)
with self.assertRaises(gfapy.TypeError):
f=fields[:]
f[8]="NM:Z:1232"
gfapy.Line("\t".join(f), vlevel = 2)
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