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import unittest
import gfapy
class TestUnitHeader(unittest.TestCase):
def test_new(self):
gfapy.line.Header(["H", "VN:Z:1.0", "xx:i:11"])
def test_string_to_gfa_line(self):
gfapy.Line("H\tVN:Z:1.0")
assert(isinstance(gfapy.Line("H\tVN:Z:1.0"),gfapy.line.Header))
self.assertEqual(gfapy.line.Header(["H", "VN:Z:1.0", "xx:i:11"]),
gfapy.Line("H\tVN:Z:1.0\txx:i:11"))
self.assertRaises(gfapy.FormatError,
gfapy.Line, "H\tH2\tVN:Z:1.0")
self.assertRaises(gfapy.TypeError,
gfapy.Line, "H\tVN:i:1.0")
def test_to_s(self):
try:
self.assertEqual("H\tVN:Z:1.0\txx:i:11",
str(gfapy.line.Header(["H", "VN:Z:1.0", "xx:i:11"])))
except:
self.assertEqual("H\txx:i:11\tVN:Z:1.0",
str(gfapy.line.Header(["H", "VN:Z:1.0", "xx:i:11"])))
def test_tag_reading(self):
self.assertEqual("1.0",
gfapy.line.Header(["H", "VN:Z:1.0", "xx:i:11"]).VN)
def test_tag_writing(self):
gfapy.line.Header(["H", "VN:Z:1.0", "xx:i:11"]).VN = "2.0"
def test_connection(self):
assert(not gfapy.line.Header(["H"]).is_connected())
assert(gfapy.Gfa().header.is_connected())
self.assertRaises(gfapy.RuntimeError,
gfapy.line.Header(["H"]).connect, gfapy.Gfa())
def test_to_gfa1_a(self):
line = gfapy.Line("H\tVN:Z:1.0\txx:i:1")
self.assertEqual("H", line._to_gfa1_a()[0])
self.assertEqual(sorted(["VN:Z:1.0", "xx:i:1"]), sorted(line._to_gfa1_a()[1:]))
line = gfapy.Line("H\tVN:Z:2.0\txx:i:1")
self.assertEqual("H", line._to_gfa1_a()[0])
self.assertEqual(sorted(["VN:Z:1.0", "xx:i:1"]), sorted(line._to_gfa1_a()[1:]))
def test_to_gfa2_a(self):
line = gfapy.Line("H\tVN:Z:1.0\txx:i:1")
self.assertEqual("H", line._to_gfa2_a()[0])
self.assertEqual(sorted(["VN:Z:2.0", "xx:i:1"]), sorted(line._to_gfa2_a()[1:]))
line = gfapy.Line("H\tVN:Z:2.0\txx:i:1")
self.assertEqual("H", line._to_gfa2_a()[0])
self.assertEqual(sorted(["VN:Z:2.0", "xx:i:1"]), sorted(line._to_gfa2_a()[1:]))
def test_add(self):
line = gfapy.Line("H\tVN:Z:2.0\txx:i:1")
line.add("yy", "test")
self.assertEqual("test", line.yy)
line.add("yy", "test")
self.assertEqual(["test","test"], line.yy)
line.add("yy", "test")
self.assertEqual(["test","test","test"], line.yy)
line.add("VN", "2.0")
self.assertEqual("2.0", line.VN)
self.assertRaises(gfapy.InconsistencyError, line.add, "VN", "1.0")
line.add("TS", "120")
self.assertEqual(120, line.TS)
line.add("TS", 120)
line.add("TS", "120")
self.assertRaises(gfapy.InconsistencyError, line.add, "TS", 130)
self.assertRaises(gfapy.InconsistencyError, line.add, "TS", "140")
def test_field_to_s(self):
line = gfapy.Line("H\tVN:Z:1.0\txx:i:1")
line.add("xx", 2)
self.assertEqual("1.0", line.field_to_s("VN"))
self.assertEqual("1\t2", line.field_to_s("xx"))
self.assertEqual("VN:Z:1.0", line.field_to_s("VN", tag=True))
self.assertEqual("xx:i:1\txx:i:2", line.field_to_s("xx", tag=True))
def test_n_duptags(self):
line = gfapy.Line("H\tVN:Z:1.0\txx:i:1")
self.assertEqual(0, line._n_duptags())
line.add("xx", 2)
self.assertEqual(1, line._n_duptags())
line.add("xx", 2)
self.assertEqual(1, line._n_duptags())
line.add("zz", 2)
self.assertEqual(1, line._n_duptags())
line.add("zz", 2)
self.assertEqual(2, line._n_duptags())
def test_split(self):
line = gfapy.Line("H\tVN:Z:1.0\txx:i:1")
line.add("xx", 2)
self.assertEqual(3, len(line._split()))
for s in line._split():
assert(isinstance(s, gfapy.line.Header))
self.assertEqual(sorted(["H\tVN:Z:1.0", "H\txx:i:1", "H\txx:i:2"]),
sorted([str(x) for x in line._split()]))
def test_merge(self):
line1 = gfapy.Line("H\tVN:Z:1.0\txx:i:1")
line2 = gfapy.Line("H\txx:i:2\tyy:f:1.0")
line1._merge(line2)
self.assertEqual("1.0", line1.VN)
self.assertEqual([1,2], line1.xx)
self.assertEqual(1.0, line1.yy)
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