def test_hemoglobin_alignment(self):
# based on example from
# http://biopython.org/DIST/docs/tutorial/Tutorial.html
hba_human = ("MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQ"
"VKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTL"
"AAHLPAEFTPAVHASLDKFLASVSTVLTSKYR")
hbb_human = ("MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAV"
"MGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNV"
"LVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH")
hba_seq = gemmi.expand_protein_one_letter_string(hba_human)
hbb_seq = gemmi.expand_protein_one_letter_string(hbb_human)
id_score = gemmi.AlignmentScoring()
id_score.match = 1
id_score.mismatch = 0
id_score.gapo = 0
id_score.gape = 0
result = gemmi.align_string_sequences(hba_seq, hbb_seq, [], id_score)
# "80 different alignments with the score 72"
self.assertEqual(result.score, 72)
blosum62 = gemmi.prepare_blosum62_scoring()
blosum62.gapo = -9
result = gemmi.align_string_sequences(hba_seq, hbb_seq, [], blosum62)
# BioPython equivalent is:
# pairwise2.align.globalds(seq1.seq, seq2.seq, blosum62, -10, -1)
self.assertEqual(result.score, 290)
def test_string_align(self):
result = gemmi.align_string_sequences(list('AABCC'), list('ABC'),
[True])
self.assertEqual(result.score, 0)
self.assertEqual(result.cigar_str(), '1I3M1I')
self.assertEqual(result.add_gaps('AABCC', 1), 'AABCC')
self.assertEqual(result.add_gaps('ABC', 2), '-ABC-')
self.assertEqual(result.calculate_identity(), 100.)
self.assertEqual(result.calculate_identity(1), 60.)
self.assertEqual(result.calculate_identity(2), 100.)
self.assertEqual(result.match_string, ' ||| ')
result = gemmi.align_string_sequences(list('SIMILARITY'),
list('PILLAR'), [])
self.assertEqual(result.match_count, 4)
self.assertEqual(result.cigar_str(), '3M1I3M3I')