def test_parse_source_seqfeature_4(self):
"""Verify source feature is parsed with no lab_host qualifier."""
self.seqfeature.qualifiers.pop("lab_host")
src_ftr = flat_files.parse_source_seqfeature(self.seqfeature)
with self.subTest():
self.assertEqual(src_ftr.lab_host, "")
with self.subTest():
self.assertEqual(src_ftr._lab_host_host_genus, "")
def test_parse_source_seqfeature_2(self):
"""Verify source feature is parsed with no organism qualifier."""
self.seqfeature.qualifiers.pop("organism")
src_ftr = flat_files.parse_source_seqfeature(self.seqfeature)
with self.subTest():
self.assertEqual(src_ftr.organism, "")
with self.subTest():
self.assertEqual(src_ftr._organism_name, "")
with self.subTest():
self.assertEqual(src_ftr._organism_host_genus, "")
def test_parse_source_seqfeature_1(self):
"""Verify source feature is parsed."""
src_ftr = flat_files.parse_source_seqfeature(self.seqfeature)
with self.subTest():
self.assertIsInstance(src_ftr.seqfeature, SeqFeature)
with self.subTest():
self.assertEqual(src_ftr.start, 2)
with self.subTest():
self.assertEqual(src_ftr.stop, 10)
with self.subTest():
self.assertEqual(src_ftr.organism, self.string1)
with self.subTest():
self.assertEqual(src_ftr.host, self.string2)
with self.subTest():
self.assertEqual(src_ftr.lab_host, self.string3)
with self.subTest():
self.assertEqual(src_ftr._organism_name, "Trixie")
with self.subTest():
self.assertEqual(src_ftr._organism_host_genus, "Mycobacterium")
with self.subTest():
self.assertEqual(src_ftr._host_host_genus, "Mycobacterium")
with self.subTest():
self.assertEqual(src_ftr._lab_host_host_genus, "Gordonia")
