def test_seqdump(self):
s = 'MELSVLLFLALLTGLLLLLVQRHPNTHDRLPPGPRPLPLLGNLLQMDRRGLLKSFLRFREKYGDVFTVHLGPRPVVMLCGVEAIREALVDKAEAFSGRGKIAMVDPFFRGYGVIFANGNRWKVLRRFSVTTMRDFGMGKRSVEERIQEEAQCLIEELRKSKGALMDPTFLFQSITANIICSIVFGKRFHYQDQEFLKMLNLFYQTFSLISSVFGQLFELFSGFLKYFPGAHRQVYKNLQEINAYIGHSVEKHRETLDPSAPKDLIDTYLLHMEKEKSNAHSEFSHQNLNLNTLSLFFAGTETTSTTLRYGFLLMLKYPHVAERVYREIEQVIGPHRPPELHDRAKMPYTEAVIYEIQRFSDLLPMGVPHIVTQHTSFRGYIIPKDTEVFLILSTALHDPHYFEKPDAFNPDHFLDANGALKKTEAFIPFSLGKRICLGEGIARAELFLFFTTILQNFSMASPVAPEDIDLTPQECGVGKIPPTYQIRFLPR'
seq = bs.ProteinSeq(
s, 'NP_000758.1 cytochrome P450 2B6 precursor [H**o sapiens]')
b = bs.blast('bioseq/res/seqdump.txt', 3)
seqs, scores = b.best_n_alignments(seq)
self.assertEqual(scores,
[484, 484, 479, 477, 453, 451, 451, 450, 449, 449])
def test_2(self):
b = bs.blast('bioseq/res/seqBlast.txt', w=11, fasta=False)
q = "cgacgacgacgacgaatgatg"
r = b.best_alignment(q)
self.assertEqual(r, (0, 0, 21, 21, 4))
def test_fasta_constructor(self):
b = bs.blast()
self.assertEqual(b.w, 3)
self.assertEqual(len(b.db), 21)
def test_1(self):
b = bs.blast('bioseq/res/seqBlast.txt', w=11, fasta=False)
q = "gacgcctcgcgctcgcgcgctgaggcaaaaaaaaaaaaaaaaaaaatcggatagctagctgagcgctcgatagcgcgttcgctgcatcgcgtatagcgctgaagctcccggcgagctgtctgtaaatcggatctcatctcgctctatcct"
r = b.best_alignment(q)
self.assertEqual(r, (1, 38, 149, 108, 3))
def test_constructor(self):
b = bs.blast('bioseq/res/seqBlast.txt', fasta=False)
self.assertEqual(b.w, 3)
self.assertEqual(b.db, self.expected_db)