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import gfapy
import unittest
class TestAPIrGfa(unittest.TestCase):
def test_adding_invalid_segment_to_rgfa(self):
gfa = gfapy.Gfa()
gfa.append("S\t1\t*")
gfa.validate()
gfa = gfapy.Gfa(dialect="rgfa")
gfa.append("S\t1\t*")
with self.assertRaises(gfapy.NotFoundError): gfa.validate()
def test_adding_containment_to_rgfa(self):
gfa = gfapy.Gfa()
gfa.append("C\t1\t+\t2\t+\t12\t*")
gfa.validate()
gfa = gfapy.Gfa(version="gfa1",dialect="rgfa")
gfa.append("C\t1\t+\t2\t+\t12\t*")
with self.assertRaises(gfapy.NotFoundError): gfa.validate()
def test_loading_examples(self):
gfapy.Gfa.from_file("tests/testdata/rgfa_example.1.gfa", dialect="rgfa")
gfapy.Gfa.from_file("tests/testdata/rgfa_example.2.gfa", dialect="rgfa")
def test_stable_sequence_names(self):
g = gfapy.Gfa.from_file("tests/testdata/rgfa_example.2.gfa", dialect="rgfa")
self.assertEqual(['smpl-Bd21_3_r.pseudomolecule_4', 'smpl-Ref.Bd4'],
sorted(g.stable_sequence_names))
g = gfapy.Gfa.from_file("tests/testdata/rgfa_example.1.gfa", dialect="rgfa")
self.assertEqual(['bar', 'chr1', 'foo'],
sorted(g.stable_sequence_names))
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