def test_sort_iterators(self):
iter1 = [{'chrom': '1', 'pos': 1}, {'chrom': '1', 'pos': 5},
{'chrom': '1', 'pos': 7}, {'chrom': '1', 'pos': 10},
{'chrom': '2', 'pos': 11}, {'chrom': '2', 'pos': 12}]
iter1 = PeekableIterator(iter(iter1))
iter2 = [{'chrom': '1', 'pos': 0}, {'chrom': '1', 'pos': 3},
{'chrom': '1', 'pos': 6}, {'chrom': '2', 'pos': 5},
{'chrom': '2', 'pos': 11}, {'chrom': '2', 'pos': 13}]
iter2 = PeekableIterator(iter(iter2))
expected = [{'chrom': '1', 'pos': 0}, {'chrom': '1', 'pos': 1},
{'chrom': '1', 'pos': 3}, {'chrom': '1', 'pos': 5},
{'chrom': '1', 'pos': 6}, {'chrom': '1', 'pos': 7},
{'chrom': '1', 'pos': 10}, {'chrom': '2', 'pos': 5},
{'chrom': '2', 'pos': 11}, {'chrom': '2', 'pos': 11},
{'chrom': '2', 'pos': 12}, {'chrom': '2', 'pos': 13}]
for x, y in zip(_sort_iterators(iter1, iter2), expected):
assert x == y
def test_peekable_iter(self):
iterator = iter(['a', 'b', 'c', 'd', 'e', 'f'])
iterator = PeekableIterator(iterator)
assert 'a' == iterator.peek()
assert 'b' == iterator.peek()
assert 'a' == next(iterator)
assert 'c' == iterator.peek()
iterator.reset_peek()
assert 'b' == iterator.peek()
assert 'b' == next(iterator)
iterator = iter(['a', 'b', 'c', 'd', 'e', 'f'])
iterator = PeekableIterator(iterator)
iterator.peek()
iterator.peek()
iterator.peek()
iterator.reset_peek()
assert 'a' == iterator.peek()
iterator = iter(['a', 'b', 'c', 'd', 'e', 'f'])
iterator = PeekableIterator(iterator)
iterator.peek()
iterator.peek()
iterator.peek()
iterator.peek()
iterator.peek()
iterator.peek()
try:
iterator.peek()
self.fail('stopIteration expected')
except StopIteration:
pass
assert 'a' == next(iterator)
iterator = iter(['a', 'b', 'c', 'd', 'e', 'f'])
iterator = PeekableIterator(iterator)
assert 'a' == iterator.peek()
assert 'a' == next(iterator)
assert 'b' == iterator.peek()
def test_peekable_iter(self):
iterator = iter(['a', 'b', 'c', 'd', 'e', 'f'])
iterator = PeekableIterator(iterator)
assert 'a' == iterator.peek()
assert 'b' == iterator.peek()
assert 'a' == next(iterator)
assert 'c' == iterator.peek()
iterator.reset_peek()
assert 'b' == iterator.peek()
assert 'b' == next(iterator)
iterator = iter(['a', 'b', 'c', 'd', 'e', 'f'])
iterator = PeekableIterator(iterator)
iterator.peek()
iterator.peek()
iterator.peek()
iterator.reset_peek()
assert 'a' == iterator.peek()
iterator = iter(['a', 'b', 'c', 'd', 'e', 'f'])
iterator = PeekableIterator(iterator)
iterator.peek()
iterator.peek()
iterator.peek()
iterator.peek()
iterator.peek()
iterator.peek()
try:
iterator.peek()
self.fail('stopIteration expected')
except StopIteration:
pass
assert 'a' == next(iterator)
iterator = iter(['a', 'b', 'c', 'd', 'e', 'f'])
iterator = PeekableIterator(iterator)
assert 'a' == iterator.peek()
assert 'a' == next(iterator)
assert 'b' == iterator.peek()
def _group_overlaping_vars(variations_1, variations_2,
ignore_2_or_more_overlaps=False,
check_ref_match=True):
if isinstance(variations_1, list) and isinstance(variations_2, list):
# This is intented only for testing and debugin
snps_1 = PeekableIterator(iter(variations_1))
snps_2 = PeekableIterator(iter(variations_2))
else:
snps_1 = PeekableIterator(_iterate_vars(variations_1))
snps_2 = PeekableIterator(_iterate_vars(variations_2))
while True:
sorted_vars = _sort_iterators(snps_1, snps_2)
region = _get_overlapping_region(sorted_vars)
snps_1.reset_peek()
snps_2.reset_peek()
snps1_in_region = _get_vars_in_region(snps_1, region)
snps2_in_region = _get_vars_in_region(snps_2, region)
snps_1.reset_peek()
snps_2.reset_peek()
if not snps1_in_region and not snps2_in_region:
break
yield (snps1_in_region, snps2_in_region)
def _group_overlaping_vars(variations_1,
variations_2,
ignore_2_or_more_overlaps=False,
check_ref_match=True):
if isinstance(variations_1, list) and isinstance(variations_2, list):
# This is intented only for testing and debugin
snps_1 = PeekableIterator(iter(variations_1))
snps_2 = PeekableIterator(iter(variations_2))
else:
snps_1 = PeekableIterator(_iterate_vars(variations_1))
snps_2 = PeekableIterator(_iterate_vars(variations_2))
while True:
sorted_vars = _sort_iterators(snps_1, snps_2)
region = _get_overlapping_region(sorted_vars)
snps_1.reset_peek()
snps_2.reset_peek()
snps1_in_region = _get_vars_in_region(snps_1, region)
snps2_in_region = _get_vars_in_region(snps_2, region)
snps_1.reset_peek()
snps_2.reset_peek()
if not snps1_in_region and not snps2_in_region:
break
yield (snps1_in_region, snps2_in_region)
