def test_sequence_alignment_instantiation(self):
test_align = biostructmap.SequenceAlignment(self.test_align)
self.assertTrue(isinstance(test_align.alignment,
Bio.Align.MultipleSeqAlignment))
for i, seq in enumerate(test_align):
#Test iteration
self.assertTrue(isinstance(seq, Bio.SeqRecord.SeqRecord))
#test _getitem__ method work to return a model object
self.assertTrue(isinstance(test_align[i], Bio.SeqRecord.SeqRecord))
def test_tajimas_d_on_sequence_alignment(self):
test_align = biostructmap.SequenceAlignment('./tests/msa/MSA_test.fsa')
#Test basic calculation of Tajima's D
taj_d = test_align.tajimas_d()
self.assertEqual(taj_d, -1.553110875316991)
#Test for errors in input to the function
with self.assertRaises(TypeError):
test_align.tajimas_d(3.5,5)
with self.assertRaises(TypeError):
test_align.tajimas_d(3,5.5)
def test_tajimas_d_on_structure_with_subset_of_reference_residues(self):
#test_sequence_alignment = AlignIO.read('./tests/msa/msa_test_86-104', 'fasta')
test_sequence_alignment = {('A',): biostructmap.SequenceAlignment(
'./tests/msa/msa_test_86-104', 'fasta')}
test_ref_dict = {('A', (' ', x+86, ' ')): ('A', (x*3 + 1, x*3 + 2, x*3 + 3)) for
x in range(18)}
test_surrounding_residues = [('A', (' ', x, ' ')) for x in range(86, 96)]
result = _tajimas_d(self.test_structure, test_sequence_alignment,
test_surrounding_residues, test_ref_dict)
self.assertEqual(result, -0.709896167879475)
def test_tajimas_d_on_structure(self):
#test_sequence_alignment = AlignIO.read('./tests/msa/msa_test_86-104', 'fasta')
test_sequence_alignment = {('A',): biostructmap.SequenceAlignment(
'./tests/msa/msa_test_86-104', 'fasta')}
test_ref_dict = {('A', (' ', x+86, ' ')): ('A', (x*3+1, x*3 + 2, x*3 + 3)) for
x in range(0, 18)}
test_surrounding_residues = [('A', (' ', x, ' ')) for x in range(86, 104)]
result = _tajimas_d(self.test_structure, test_sequence_alignment,
test_surrounding_residues, test_ref_dict)
self.assertEqual(result, -0.7801229937910628)
def setUp(self):
self.test_file = './tests/pdb/1zrl.pdb'
self.structure = biostructmap.Structure(self.test_file)
self.test_align = './tests/msa/protein_MSA_1zrl.fsa'
self.msa = biostructmap.SequenceAlignment(self.test_align)
ref_seq = ('MKCNISIYFFASFFVLYFAKARNEYDIKENEKFLDVYKEKFNELDKKKYGNVQKTDKKIFTFIENKLDILNNSKFNKRWK'
'SYGTPDNIDKNMSLINKHNNEEMFNNNYQSFLSTSSLIKQNKYVPINAVRVSRILSFLDSRINNGRNTSSNNEVLSNCRE'
'KRKGMKWDCKKKNDRSNYVCIPDRRIQLCIVNLSIIKTYTKETMKDHFIEASKKESQLLLKKNDNKYNSKFCNDLKNSFL'
'DYGHLAMGNDMDFGGYSTKAENKIQEVFKGAHGEISEHKIKNFRKKWWNEFREKLWEAMLSEHKNNINNCKNIPQEELQI'
'TQWIKEWHGEFLLERDNRSKLPKSKCKNNTLYEACEKECIDPCMKYRDWIIRSKFEWHTLSKEYETQKVPKENAENYLIK'
'ISENKNDAKVSLLLNNCDAEYSKYCDCKHTTTLVKSVLNGNDNTIKEKREHIDLDDFSKFGCDKNSVDTNTKVWECKKPY'
'KLSTKDVCVPPRRQELCLGNIDRIYDKNLLMIKEHILAIAIYESRILKRKYKNKDDKEVCKIINKTFADIRDIIGGTDYW'
'NDLSNRKLVGKINTNSNYVHRNKQNDKLFRDEWWKVIKKDVWNVISWVFKDKTVCKEDDIENIPQFFRWFSEWGDDYCQD'
'KTKMIETLKVECKEKPCEDDNCKRKCNSYKEWISKKKEEYNKQAKQYQEYQKGNNYKMYSEFKSIKPEVYLKKYSEKCSN'
'LNFEDEFKEELHSDYKNKCTMCPEVKDVPISIIRNNEQTS')
self.reference_seqs = {'A': ref_seq}
def test_tajimas_d_on_long_sequence(self):
test_align = biostructmap.SequenceAlignment('./tests/msa/MSA_test_long.fsa')
taj_d = test_align.tajimas_d()
self.assertEqual(taj_d, 0.33458440732186856)
def setUp(self):
self.test_file = './tests/msa/MSA_test.fsa'
self.alignment = AlignIO.read(self.test_file, 'fasta')
self.biostructmap_alignment = biostructmap.SequenceAlignment('./tests/msa/MSA_test.fsa')
self.varsites = seqtools._var_site(self.alignment)