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import gfapy
import unittest
class TestApiVersion(unittest.TestCase):
def test_init_without_version_by_init(self):
gfa = gfapy.Gfa()
self.assertEqual(None, gfa.version)
def test_init_GFA1(self):
gfa = gfapy.Gfa(version="gfa1")
self.assertEqual("gfa1", gfa.version)
def test_init_GFA2(self):
gfa = gfapy.Gfa(version="gfa2")
self.assertEqual("gfa2", gfa.version)
def test_init_invalid_version(self):
self.assertRaises(gfapy.VersionError, gfapy.Gfa, version="x.x")
def test_GFA1_header(self):
hother = "H\taa:A:a\tff:f:1.1"
hv1 = "H\tzz:Z:test\tVN:Z:1.0\tii:i:11"
gfa = gfapy.Gfa()
gfa.add_line(hother)
self.assertEqual(None, gfa.version)
gfa.add_line(hv1)
self.assertEqual("gfa1", gfa.version)
def test_GFA2_header(self):
hother = "H\taa:A:a\tff:f:1.1"
hv2 = "H\tzz:Z:test\tVN:Z:2.0\tii:i:11"
gfa = gfapy.Gfa()
gfa.add_line(hother)
self.assertEqual(None, gfa.version)
gfa.add_line(hv2)
self.assertEqual("gfa2", gfa.version)
def test_unknown_version_in_header(self):
hother = "H\taa:A:a\tff:f:1.1"
hvx = "H\tzz:Z:test\tVN:Z:x.x\tii:i:11"
gfa = gfapy.Gfa()
gfa.add_line(hother)
self.assertEqual(None, gfa.version)
self.assertRaises(gfapy.VersionError, gfa.add_line, hvx)
def test_wrong_version_in_header(self):
hother = "H\taa:A:a\tff:f:1.1"
hv2 = "H\tzz:Z:test\tVN:Z:2.0\tii:i:11"
gfa = gfapy.Gfa(version="gfa1")
gfa.add_line(hother)
self.assertEqual("gfa1", gfa.version)
self.assertRaises(gfapy.VersionError, gfa.add_line, hv2)
def test_conflicting_versions_in_header(self):
hother = "H\taa:A:a\tff:f:1.1"
hv1 = "H\tzz:Z:test\tVN:Z:1.0\tii:i:11"
hv2 = "H\tzz:Z:test\tVN:Z:2.0\tii:i:11"
gfa = gfapy.Gfa()
gfa.add_line(hother)
gfa.add_line(hv1)
self.assertRaises(gfapy.VersionError, gfa.add_line, hv2)
def test_version_by_segment_GFA1_syntax(self):
sv1 = "S\tA\t*"
gfa = gfapy.Gfa()
gfa.add_line(sv1)
self.assertEqual("gfa1", gfa.version)
def test_version_by_segment_GFA2_syntax(self):
sv2 = "S\tB\t100\t*"
gfa = gfapy.Gfa()
gfa.add_line(sv2)
self.assertEqual("gfa2", gfa.version)
def test_GFA2_segment_in_GFA1(self):
sv1 = "S\tA\t*"
sv2 = "S\tB\t100\t*"
gfa = gfapy.Gfa()
gfa.add_line(sv1)
self.assertRaises(gfapy.VersionError, gfa.add_line, sv2)
def test_GFA1_segment_in_GFA2(self):
sv1 = "S\tA\t*"
sv2 = "S\tB\t100\t*"
gfa = gfapy.Gfa()
gfa.add_line(sv2)
self.assertRaises(gfapy.VersionError, gfa.add_line, sv1)
def test_version_by_GFA2_specific_line_E(self):
e = "E\t*\tA+\tB+\t0\t10\t20\t30\t*"
gfa = gfapy.Gfa()
gfa.add_line(e)
self.assertEqual("gfa2", gfa.version)
def test_version_by_GFA2_specific_line_G(self):
g = "G\t*\tA+\tB-\t1000\t*"
gfa = gfapy.Gfa()
gfa.add_line(g)
self.assertEqual("gfa2", gfa.version)
def test_version_by_GFA2_specific_line_F(self):
f = "F\tX\tID+\t10\t100\t0\t90$\t*"
gfa = gfapy.Gfa()
gfa.add_line(f)
self.assertEqual("gfa2", gfa.version)
def test_version_by_GFA2_specific_line_O(self):
o = "O\tX\tA+ B- C+"
gfa = gfapy.Gfa()
gfa.add_line(o)
self.assertEqual("gfa2", gfa.version)
def test_version_by_GFA2_specific_line_U(self):
u = "U\tX\tA B C"
gfa = gfapy.Gfa()
gfa.add_line(u)
self.assertEqual("gfa2", gfa.version)
def test_version_guess_GFA1_specific_line_L(self):
string = "L\tA\t-\tB\t+\t*"
gfa = gfapy.Gfa()
gfa.add_line(string)
gfa.process_line_queue()
self.assertEqual("gfa1", gfa.version)
def test_version_guess_GFA1_specific_line_C(self):
string = "C\tA\t+\tB\t-\t10\t*"
gfa = gfapy.Gfa()
gfa.add_line(string)
gfa.process_line_queue()
self.assertEqual("gfa1", gfa.version)
def test_version_guess_GFA1_specific_line_P(self):
string = "P\t1\ta-,b+\t*"
gfa = gfapy.Gfa()
gfa.add_line(string)
gfa.process_line_queue()
self.assertEqual("gfa1", gfa.version)
def test_version_guess_default(self):
gfa = gfapy.Gfa()
gfa.process_line_queue()
self.assertEqual("gfa2", gfa.version)
def test_header_version(self):
self.assertEqual("generic", gfapy.Line("H\tVN:Z:1.0").version)
self.assertEqual("gfa1", gfapy.Line("H\tVN:Z:1.0", version="gfa1").version)
self.assertEqual("gfa2", gfapy.Line("H\tVN:Z:1.0", version="gfa2").version)
def test_comment_version(self):
self.assertEqual("generic", gfapy.Line("# VN:Z:1.0").version)
self.assertEqual("gfa1", gfapy.Line("# VN:Z:1.0", version="gfa1").version)
self.assertEqual("gfa2", gfapy.Line("# VN:Z:1.0", version="gfa2").version)
def test_segment_version(self):
self.assertEqual("gfa1", gfapy.Line("S\tA\tNNNN").version)
self.assertEqual("gfa2", gfapy.Line("S\tA\t1\tNNNN").version)
self.assertEqual("gfa1", gfapy.Line("S\tA\tNNNN", version="gfa1").version)
self.assertEqual("gfa2", gfapy.Line("S\tA\t1\tNNNN", version="gfa2").version)
self.assertRaises(gfapy.FormatError,
gfapy.Line, "S\tA\t1\tNNNN", version="gfa1")
self.assertRaises(gfapy.FormatError,
gfapy.Line, "S\tA\tNNNN", version="gfa2")
def test_link_version(self):
string = "L\tA\t+\tB\t-\t*"
self.assertEqual("gfa1", gfapy.Line(string).version)
self.assertEqual("gfa1", gfapy.Line(string, version="gfa1").version)
self.assertRaises(gfapy.VersionError, gfapy.Line, string, version="gfa2")
self.assertRaises(gfapy.VersionError,
gfapy.line.edge.Link, ["A","+","B","-","*"], version="gfa2")
def test_containment_version(self):
string = "C\tA\t+\tB\t-\t10\t*"
self.assertEqual("gfa1", gfapy.Line(string).version)
self.assertEqual("gfa1", gfapy.Line(string,version="gfa1").version)
self.assertRaises(gfapy.VersionError, gfapy.Line,string,version="gfa2")
self.assertRaises(gfapy.VersionError, gfapy.line.edge.Containment,
["A","+","B","-","10","*"], version="gfa2")
def test_edge_version(self):
self.assertEqual("gfa2", gfapy.Line("E\t*\tA-\tB+\t0\t100\t0\t100\t*").version)
self.assertEqual("gfa2", gfapy.Line("E\t*\tA-\tB+\t0\t100\t0\t100\t*",version=\
"gfa2").version)
self.assertRaises(gfapy.VersionError,
gfapy.Line, "E\t*\tA-\tB+\t0\t100\t0\t100\t*", version="gfa1")
self.assertRaises(gfapy.VersionError,
gfapy.line.edge.GFA2, ["A-","B+", "0", "100", "0", "100", "*"],
version="gfa1")
def test_gap_version(self):
self.assertEqual("gfa2", gfapy.Line("G\t*\tA-\tB+\t100\t*").version)
self.assertEqual("gfa2", gfapy.Line("G\t*\tA-\tB+\t100\t*",
version="gfa2").version)
self.assertRaises(gfapy.VersionError,
gfapy.Line, "G\t*\tA-\tB+\t100\t*", version="gfa1")
self.assertRaises(gfapy.VersionError,
gfapy.line.Gap,["A-","B+", "100", "*"], version="gfa1")
def test_fragment_version(self):
self.assertEqual("gfa2", gfapy.Line("F\tA\tread1-\t0\t100\t0\t100\t*").version)
self.assertEqual("gfa2", gfapy.Line("F\tA\tread1-\t0\t100\t0\t100\t*", version=\
"gfa2").version)
self.assertRaises(gfapy.VersionError,
gfapy.Line, "F\tA\tread1-\t0\t100\t0\t100\t*", version="gfa1")
self.assertRaises(gfapy.VersionError,
gfapy.line.Fragment,["A","read-", "0", "100", "0", "100", "*"],
version="gfa1")
def test_custom_record_version(self):
self.assertEqual("gfa2", gfapy.Line("X\tVN:Z:1.0").version)
self.assertEqual("gfa2", gfapy.Line("X\tVN:Z:1.0", version="gfa2").version)
self.assertRaises(gfapy.VersionError,
gfapy.Line, "X\tVN:Z:1.0", version="gfa1")
self.assertRaises(gfapy.VersionError,
gfapy.line.CustomRecord, ["X","VN:Z:1.0"], version="gfa1")
def test_path_version(self):
string = "P\t1\tA+,B-\t*"
self.assertEqual("gfa1", gfapy.Line(string).version)
self.assertEqual("gfa1", gfapy.Line(string, version="gfa1").version)
self.assertRaises(gfapy.VersionError, gfapy.Line, string, version="gfa2")
string = "O\t1\tA+ B-"
self.assertEqual("gfa2", gfapy.Line(string).version)
self.assertEqual("gfa2", gfapy.Line(string, version="gfa2").version)
self.assertRaises(gfapy.VersionError, gfapy.Line, string, version="gfa1")
def test_set_version(self):
string = "U\t1\tA B C"
self.assertEqual("gfa2", gfapy.Line(string).version)
self.assertEqual("gfa2", gfapy.Line(string, version="gfa2").version)
self.assertRaises(gfapy.VersionError, gfapy.Line, string, version="gfa1")
def test_unknown_record_version(self):
self.assertEqual("gfa2", gfapy.line.Unknown([None, "A"]).version)
self.assertEqual("gfa2", gfapy.line.Unknown([None, "A"], version="gfa2").version)
self.assertRaises(gfapy.VersionError, gfapy.line.Unknown,["\n","A"], version="gfa1")
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