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import utils
import os
import unittest
import urllib.request
TOPDIR = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))
utils.set_search_paths(TOPDIR)
import ihm.reference
class Tests(unittest.TestCase):
def test_reference(self):
"""Test Reference base class"""
_ = ihm.reference.Reference() # noop
def test_sequence(self):
"""Test Sequence class"""
s = ihm.reference.Sequence(
db_name='testdb', db_code='testcode', accession='testacc',
sequence='CCCG', details='foo')
s.alignments.append(ihm.reference.Alignment(
db_begin=10, db_end=30, entity_begin=20, entity_end=40))
self.assertEqual(s.db_name, 'testdb')
self.assertEqual(s.db_code, 'testcode')
self.assertEqual(s.accession, 'testacc')
self.assertEqual(s.sequence, 'CCCG')
self.assertEqual(s.details, 'foo')
a, = s._get_alignments()
self.assertEqual(a.db_begin, 10)
self.assertEqual(a.db_end, 30)
self.assertEqual(a.entity_begin, 20)
self.assertEqual(a.entity_end, 40)
self.assertEqual(a.seq_dif, [])
def test_sequence_default_alignment(self):
"""Test Sequence class with default Alignment"""
s = ihm.reference.Sequence(
db_name='testdb', db_code='testcode',
accession='testacc', sequence='CCCG', details='foo')
self.assertEqual(s.db_name, 'testdb')
self.assertEqual(s.db_code, 'testcode')
self.assertEqual(s.accession, 'testacc')
self.assertEqual(s.sequence, 'CCCG')
self.assertEqual(s.details, 'foo')
a1, = s._get_alignments()
a1a, = s._get_alignments()
# should get same default alignment each time (get cache 2nd time)
self.assertEqual(id(a1), id(a1a))
self.assertEqual(a1.db_begin, 1)
self.assertIsNone(a1.db_end)
self.assertEqual(a1.entity_begin, 1)
self.assertIsNone(a1.entity_end)
self.assertEqual(a1.seq_dif, [])
def test_uniprot_sequence(self):
"""Test UniProtSequence class"""
lpep = ihm.LPeptideAlphabet()
sd = ihm.reference.SeqDif(seq_id=1, db_monomer=lpep['C'],
monomer=lpep['W'], details='Test mutation')
s = ihm.reference.UniProtSequence(
db_code='testcode', accession='testacc', sequence='CCCG')
s.alignments.append(ihm.reference.Alignment(seq_dif=[sd]))
self.assertEqual(s.db_name, 'UNP')
self.assertEqual(s.db_code, 'testcode')
self.assertEqual(s.accession, 'testacc')
self.assertEqual(s.sequence, 'CCCG')
self.assertIsNone(s.details)
a, = s.alignments
self.assertEqual(len(a.seq_dif), 1)
self.assertEqual(a.seq_dif[0].seq_id, 1)
self.assertEqual(a.seq_dif[0].db_monomer.id, 'CYS')
self.assertEqual(a.seq_dif[0].monomer.id, 'TRP')
self.assertEqual(a.seq_dif[0].details, 'Test mutation')
def _get_from_uniprot_accession(self, fasta_fname):
def mock_urlopen(url):
self.assertTrue(url.endswith('/testacc.fasta'))
fname = utils.get_input_file_name(TOPDIR, fasta_fname)
return open(fname, 'rb')
# Need to mock out urllib.request so we don't hit the network
# (expensive) every time we test
try:
orig_urlopen = urllib.request.urlopen
urllib.request.urlopen = mock_urlopen
return ihm.reference.UniProtSequence.from_accession('testacc')
finally:
urllib.request.urlopen = orig_urlopen
def test_uniprot_sequence_from_accession(self):
"""Test UniProtSequence.from_accession()"""
r = self._get_from_uniprot_accession('P52891.fasta')
self.assertIsInstance(r, ihm.reference.UniProtSequence)
self.assertEqual(r.db_code, 'NUP84_YEAST')
self.assertEqual(r.accession, 'testacc')
self.assertEqual(len(r.sequence), 726)
self.assertEqual(r.sequence[:20], 'MELSPTYQTERFTKFSDTLK')
self.assertEqual(
r.details,
'Nucleoporin NUP84 OS=Saccharomyces cerevisiae (strain ATCC '
'204508 / S288c) OX=559292 GN=NUP84 PE=1 SV=1')
def test_uniprot_sequence_from_accession_bad_header(self):
"""Test UniProtSequence.from_accession() with bad header"""
self.assertRaises(ValueError, self._get_from_uniprot_accession,
'uniprot_bad_header.fasta')
def test_uniprot_sequence_from_accession_no_details(self):
"""Test UniProtSequence.from_accession() with no details"""
r = self._get_from_uniprot_accession('uniprot_no_details.fasta')
self.assertIsInstance(r, ihm.reference.UniProtSequence)
self.assertEqual(r.db_code, 'NUP84_YEAST')
self.assertEqual(r.accession, 'testacc')
self.assertEqual(len(r.sequence), 726)
self.assertEqual(r.sequence[:20], 'MELSPTYQTERFTKFSDTLK')
self.assertIsNone(r.details)
if __name__ == '__main__':
unittest.main()
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