def test_left(self):
chrom, pos, orient1, orient2, ref, seq = _parse_bnd_alt('G]10:198982]')
self.assertEqual('10', chrom)
self.assertEqual(198982, pos)
self.assertEqual(ORIENT.LEFT, orient1)
self.assertEqual(ORIENT.LEFT, orient2)
self.assertEqual('', seq)
self.assertEqual('G', ref)
chrom, pos, orient1, orient2, ref, seq = _parse_bnd_alt(']10:198982]G')
self.assertEqual('10', chrom)
self.assertEqual(198982, pos)
self.assertEqual(ORIENT.LEFT, orient2)
self.assertEqual('', seq)
self.assertEqual('G', ref)
def test_alternate_chrom(self):
chrom, pos, orient1, orient2, ref, seq = _parse_bnd_alt('G]GL000.01:198982]')
self.assertEqual('GL000.01', chrom)
self.assertEqual(198982, pos)
self.assertEqual(ORIENT.LEFT, orient2)
self.assertEqual('', seq)
self.assertEqual('G', ref)
def test_right(self):
# '[4:190898243[AGGT'
chrom, pos, orient1, orient2, ref, seq = _parse_bnd_alt('[4:190898243[A')
self.assertEqual('4', chrom)
self.assertEqual(190898243, pos)
self.assertEqual(ORIENT.RIGHT, orient1)
self.assertEqual(ORIENT.RIGHT, orient2)
self.assertEqual('', seq)
self.assertEqual('A', ref)
def test_left_untemp_seq(self):
chrom, pos, orient1, orient2, ref, seq = _parse_bnd_alt(']11:123456]AGTNNNCAT')
self.assertEqual('11', chrom)
self.assertEqual(123456, pos)
self.assertEqual(ORIENT.LEFT, orient2)
self.assertEqual('AGTNNNCA', seq)
self.assertEqual('T', ref)
chrom, pos, orient1, orient2, ref, seq = _parse_bnd_alt(']8:1682443]TGC')
self.assertEqual('8', chrom)
self.assertEqual(1682443, pos)
self.assertEqual(ORIENT.LEFT, orient2)
self.assertEqual('TG', seq)
self.assertEqual('C', ref)
chrom, pos, orient1, orient2, ref, seq = _parse_bnd_alt('AAGTG]11:66289601]')
self.assertEqual('11', chrom)
self.assertEqual(66289601, pos)
self.assertEqual(ORIENT.LEFT, orient2)
self.assertEqual('AGTG', seq)
self.assertEqual('A', ref)
def test_right_untemp_seq(self):
chrom, pos, orient1, orient2, ref, seq = _parse_bnd_alt('[5:190898243[AGGT')
self.assertEqual('5', chrom)
self.assertEqual(190898243, pos)
self.assertEqual(ORIENT.RIGHT, orient1)
self.assertEqual(ORIENT.RIGHT, orient2)
self.assertEqual('AGG', seq)
self.assertEqual('T', ref)
chrom, pos, orient1, orient2, ref, seq = _parse_bnd_alt('CAGTNNNCA[5:190898243[')
self.assertEqual('5', chrom)
self.assertEqual(190898243, pos)
self.assertEqual(ORIENT.LEFT, orient1)
self.assertEqual(ORIENT.RIGHT, orient2)
self.assertEqual('AGTNNNCA', seq)
self.assertEqual('C', ref)
chrom, pos, orient1, orient2, ref, seq = _parse_bnd_alt('CTG[21:47575965[')
self.assertEqual('21', chrom)
self.assertEqual(47575965, pos)
self.assertEqual(ORIENT.LEFT, orient1)
self.assertEqual(ORIENT.RIGHT, orient2)
self.assertEqual('TG', seq)
self.assertEqual('C', ref)