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import gfapy
import unittest
class TestLinePath(unittest.TestCase):
def test_from_string(self):
fields = ["P","4","1+,2-,3+","9M2I3D1M,12M","ab:Z:abcd"]
string = "\t".join(fields)
gfapy.Line(string)
self.assertIsInstance(gfapy.Line(string), gfapy.line.group.Path)
self.assertEqual(str(fields[0]), gfapy.Line(string).record_type)
self.assertEqual(str(fields[1]), gfapy.Line(string).path_name)
self.assertEqual([gfapy.OrientedLine("1","+"),
gfapy.OrientedLine("2","-"),
gfapy.OrientedLine("3","+")],
gfapy.Line(string).segment_names)
self.assertEqual([[gfapy.alignment.cigar.Operation(9,"M"),
gfapy.alignment.cigar.Operation(2,"I"),
gfapy.alignment.cigar.Operation(3,"D"),
gfapy.alignment.cigar.Operation(1,"M")],
[gfapy.alignment.cigar.Operation(12,"M")]],
gfapy.Line(string).overlaps)
self.assertEqual("abcd", gfapy.Line(string).ab)
with self.assertRaises(gfapy.FormatError):
gfapy.Line(string+"\tH1")
with self.assertRaises(gfapy.FormatError):
gfapy.Line("P\tH")
with self.assertRaises(gfapy.FormatError):
f=fields[:]
f[2]="1,2,3"
gfapy.Line("\t".join(f), vlevel = 2)
with self.assertRaises(gfapy.InconsistencyError):
f=fields[:]
f[2]="1+,2+"
f[3]="9M,12M,3M"
gfapy.Line("\t".join(f), vlevel = 2)
f=fields[:]
f[3]="*,*"
gfapy.Line("\t".join(f), vlevel = 2)
f=fields[:]
f[3]="9M2I3D1M,12M,12M"
gfapy.Line("\t".join(f), vlevel = 2)
f=fields[:]
f[3]="*"
gfapy.Line("\t".join(f), vlevel = 2)
with self.assertRaises(gfapy.FormatError):
f=fields[:]
f[3]="12,12"
gfapy.Line("\t".join(f), vlevel = 2)
with self.assertRaises(gfapy.FormatError):
f=fields[:]
f[3]="12M|12M"
gfapy.Line("\t".join(f), vlevel = 2)
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