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