def test_open_intervals(self):
assert P.to_data(P.open(-P.inf, P.inf)) == [(False, float('-inf'),
float('inf'), False)]
assert P.to_data(P.openclosed(-P.inf,
0)) == [(False, float('-inf'), 0, True)]
assert P.to_data(P.closedopen(0, P.inf)) == [(True, 0, float('inf'),
False)]
def test_identity(self):
i1, i2, i3, i4 = P.closed(0, 1), P.openclosed(0, 1), P.closedopen(0, 1), P.open(0, 1)
assert P.from_data(P.to_data(i2)) == i2
assert P.from_data(P.to_data(i3)) == i3
assert P.from_data(P.to_data(i4)) == i4
assert P.from_data(P.to_data(i1)) == i1
def make_POS_and_CIGAR(stitched_m):
CIGAR = ''
conflict = False
interval_list = []
ref_and_skip_intersect = stitched_m['ref_intervals'] & stitched_m[
'skipped_intervals']
nreads_conflict = 0
if not ref_and_skip_intersect.empty:
conflict = True
nreads_conflict = len(list(P.iterate(ref_and_skip_intersect, step=1)))
stitched_m['skipped_intervals'] = stitched_m[
'skipped_intervals'] - ref_and_skip_intersect
interval_list = [
i for t in P.to_data(ref_and_skip_intersect) for i in t[1:-1]
]
ref_tuples = [(i[1] if i[0] else i[1] + 1, i[2] if i[3] else i[2] - 1)
for i in P.to_data(stitched_m['ref_intervals'])]
if stitched_m['skipped_intervals'].empty:
skipped_tuples = []
else:
skipped_tuples = [(i[1] if i[0] else i[1] + 1,
i[2] if i[3] else i[2] - 1)
for i in P.to_data(stitched_m['skipped_intervals'])]
if stitched_m['del_intervals'].empty:
del_tuples = []
else:
del_tuples = [(i[1] if i[0] else i[1] + 1, i[2] if i[3] else i[2] - 1)
for i in P.to_data(stitched_m['del_intervals'])[1:-1]]
POS = ref_tuples[0][0] + 1
tuple_dict = {'M': ref_tuples, 'N': skipped_tuples, 'D': del_tuples}
while sum(len(t) for t in tuple_dict.values()) > 0:
pos_dict = {k: v[0][0] for k, v in tuple_dict.items() if len(v) > 0}
c = min(pos_dict, key=pos_dict.get)
n_bases = np.int_(tuple_dict[c[0]][0][1] - tuple_dict[c[0]][0][0]) + 1
if n_bases == 0:
del tuple_dict[c[0]][0]
continue
CIGAR += '{}{}'.format(n_bases, c[0])
del tuple_dict[c[0]][0]
return POS, CIGAR, conflict, nreads_conflict, interval_list
def keys(iv):
return tuple(tuple(int(e) for e in d[1:3]) for d in to_data(iv))
def test_parameters(self):
i = P.openclosed(-P.inf, 4) | P.closedopen(6, P.inf)
assert P.to_data(i, conv=str, pinf='highest', ninf='lowest') == [(False, 'lowest', '4', True), (True, '6', 'highest', False)]
def test_unions(self):
i = P.openclosed(-P.inf, 4) | P.closedopen(6, P.inf)
assert P.to_data(i) == [(False, float('-inf'), 4, True), (True, 6, float('inf'), False)]
def test_empty_interval(self):
assert P.to_data(P.empty()) == [(False, float('inf'), float('-inf'), False)]
def test_singleton(self):
assert P.to_data(P.singleton(0)) == [(True, 0, 0, True)]
def test_values(self):
assert P.to_data(P.closed('a', 'b')) == [(True, 'a', 'b', True)]
assert P.to_data(P.closed(tuple([0]), tuple([1]))) == [(True, (0,), (1,), True)]
def test_bounds(self):
assert P.to_data(P.closed(0, 1)) == [(True, 0, 1, True)]
assert P.to_data(P.openclosed(0, 1)) == [(False, 0, 1, True)]
assert P.to_data(P.closedopen(0, 1)) == [(True, 0, 1, False)]
assert P.to_data(P.open(0, 1)) == [(False, 0, 1, False)]