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import gfapy
import unittest
class TestAPIGfaBasics(unittest.TestCase):
def test_initialize(self):
gfapy.Gfa() # nothing raised
gfa = gfapy.Gfa()
self.assertEqual(gfapy.Gfa, gfa.__class__)
def test_version_empty(self):
gfa = gfapy.Gfa()
self.assertIsNone(gfa.version)
gfa = gfapy.Gfa(version="gfa1")
self.assertEqual("gfa1", gfa.version)
gfa = gfapy.Gfa(version="gfa2")
self.assertEqual("gfa2", gfa.version)
with self.assertRaises(gfapy.VersionError): gfapy.Gfa(version="0.0")
def test_validate(self):
gfa = gfapy.Gfa(version="gfa1")
gfa.append("S\t1\t*")
gfa.validate() # nothing raised
gfa.append("L\t1\t+\t2\t-\t*")
with self.assertRaises(gfapy.NotFoundError): gfa.validate()
gfa.append("S\t2\t*")
gfa.validate() # nothing raised
gfa.append("P\t3\t1+,4-\t*")
with self.assertRaises(gfapy.NotFoundError): gfa.validate()
gfa.append("S\t4\t*")
with self.assertRaises(gfapy.NotFoundError): gfa.validate()
gfa.append("L\t4\t+\t1\t-\t*")
gfa.validate() # nothing raised
def test_to_s(self):
lines = ["H\tVN:Z:1.0","S\t1\t*","S\t2\t*","S\t3\t*",
"L\t1\t+\t2\t-\t*","C\t1\t+\t3\t-\t12\t*","P\t4\t1+,2-\t*"]
gfa = gfapy.Gfa()
for l in lines: gfa.append(l)
self.assertEqual(set(lines), set(str(gfa).split("\n")))
## def test_from_file(self):
## filename = "tests/testdata/example1.gfa"
## gfa = gfapy.Gfa.from_file(filename)
## assert(gfa)
## with open(filename) as f:
## txt = f.read()
## self.assertEqual(txt, str(gfa))
## def test_to_file(self):
## filename = "tests/testdata/example1.gfa"
## gfa = gfapy.Gfa.from_file(filename)
## tmp = Tempfile("example1")
## gfa.to_file(tmp.path)
## tmp.rewind
## self.assertEqual(IO.read(filename), IO.read(tmp))
def test_from_string(self):
lines = ["H\tVN:Z:1.0","S\t1\t*","S\t2\t*","S\t3\t*",
"L\t1\t+\t2\t-\t*","C\t1\t+\t3\t-\t12\t*","P\t4\t1+,2-\t*"]
gfa1 = gfapy.Gfa()
for l in lines: gfa1.append(l)
gfa2 = gfapy.Gfa("\n".join(lines))
assert(gfa2)
self.assertEqual(gfapy.Gfa, gfa2.__class__)
self.assertEqual(str(gfa1), str(gfa2))
def test_from_list(self):
lines = ["H\tVN:Z:1.0","S\t1\t*","S\t2\t*","S\t3\t*",
"L\t1\t+\t2\t-\t*","C\t1\t+\t3\t-\t12\t*","P\t4\t1+,2-\t*"]
gfa1 = gfapy.Gfa()
for l in lines: gfa1.append(l)
gfa2 = gfapy.Gfa(lines)
assert(gfa2)
self.assertEqual(gfapy.Gfa, gfa2.__class__)
self.assertEqual(str(gfa1), str(gfa2))
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