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import unittest
import gfapy
class TestUnitLine(unittest.TestCase):
def test_initialize_not_enough_positional_fields(self):
gfapy.Line(["S", "1", "*"])
with self.assertRaises(gfapy.FormatError):
gfapy.Line(["S", "1"])
def test_initialize_too_many_positionals(self):
with self.assertRaises(gfapy.FormatError):
gfapy.Line(["S", "1", "*", "*"])
def test_initialize_predefined_tag_wrong_type(self):
gfapy.line.Header(["H", "VN:Z:1"])
with self.assertRaises(gfapy.TypeError):
gfapy.line.Header(["H", "VN:i:1"])
def test_initialize_wrong_tag_format(self):
with self.assertRaises(gfapy.FormatError):
gfapy.line.Header(["H", "VN i:1"])
def test_initialize_positional_field_type_error(self):
with self.assertRaises(gfapy.FormatError):
gfapy.line.segment.GFA1(["S", "1\t1", "*", "*"])
def test_initialize_tag_type_error(self):
with self.assertRaises(gfapy.FormatError):
gfapy.line.Header(["H", "zz:i:1A"])
def test_initialize_duplicate_tag(self):
with self.assertRaises(gfapy.NotUniqueError):
gfapy.line.Header(["H", "zz:i:1", "zz:i:2"])
with self.assertRaises(gfapy.NotUniqueError):
gfapy.line.Header(["H", "zz:i:1", "VN:Z:1", "zz:i:2"])
def test_initialize_custom_tag(self):
with self.assertRaises(gfapy.FormatError):
gfapy.line.Header(["H", "ZZ:Z:1"])
def test_record_type(self):
l = gfapy.line.Header(["H", "xx:i:13", "VN:Z:HI"])
self.assertEqual("H", l.record_type)
with self.assertRaises(AttributeError):
l.record_type = "S"
def test_add_tag(self):
l = gfapy.line.Header(["H", "xx:i:13", "VN:Z:HI"])
self.assertEqual(None, l.xy)
l.set("xy", "HI")
self.assertEqual("HI", l.xy)
def test_unknown_record_type(self):
with self.assertRaises(gfapy.VersionError):
gfapy.Line("Z\txxx", version = "gfa1")
gfapy.Line("Z\txxx", version = "gfa2")
gfapy.Line("Z\txxx")
def test_field_alias(self):
s = gfapy.Line("S\tA\t*")
self.assertEqual(s.name, s.get("name"))
self.assertEqual("A", s.name)
self.assertEqual("A", s.sid)
self.assertEqual("A", s.get("name"))
self.assertEqual("A", s.get("sid"))
s.set("name", "B")
self.assertEqual("B", s.get("sid"))
s.set("sid", "C")
self.assertEqual("C", s.name)
def test_to_s(self):
fields = ["H", "VN:Z:HI", "xx:i:13"]
l = gfapy.line.Header(fields[:])
lstr = str(l)
self.assertEqual("\t".join(fields), lstr)
def test_clone(self):
l = gfapy.Line("H\tVN:Z:1.0")
l1 = l
l2 = l.clone()
self.assertIsInstance(l, gfapy.line.Header)
self.assertIsInstance(l2, gfapy.line.Header)
l2.VN = "2.0"
self.assertEqual("2.0", l2.VN)
self.assertEqual("1.0", l.VN)
l1.VN = "2.0"
self.assertEqual("2.0", l.VN)
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