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")