def test_sort_ranges(self):
contigs = [
reference_pb2.ContigInfo(name='c', n_bases=100, pos_in_fasta=0),
reference_pb2.ContigInfo(name='a', n_bases=76, pos_in_fasta=1),
reference_pb2.ContigInfo(name='b', n_bases=121, pos_in_fasta=2),
]
unsorted = ranges.parse_literals(
['a:10', 'c:20', 'b:30', 'b:10-15', 'b:10', 'a:5'])
# Without contigs we sort the contigs by name lexicographically.
self.assertEqual(
ranges.parse_literals(
['a:5', 'a:10', 'b:10', 'b:10-15', 'b:30', 'c:20']),
ranges.sorted_ranges(unsorted))
# With contigs we sort by the position of the contigs themselves.
self.assertEqual(
ranges.parse_literals(
['c:20', 'a:5', 'a:10', 'b:10', 'b:10-15', 'b:30']),
ranges.sorted_ranges(unsorted, contigs))
def test_rangeset_iteration_order(self):
contigs = [
reference_pb2.ContigInfo(name='c', n_bases=100, pos_in_fasta=0),
reference_pb2.ContigInfo(name='b', n_bases=121, pos_in_fasta=2),
reference_pb2.ContigInfo(name='a', n_bases=76, pos_in_fasta=1),
]
unsorted = ranges.parse_literals(
['a:10', 'c:20', 'b:30', 'b:10-15', 'a:5'])
# Iteration order over a RangeSet instantiated with a contigs list is
# determined by pos_in_fasta, start, end.
range_set_with_contigs = ranges.RangeSet(unsorted, contigs)
self.assertEqual(
ranges.parse_literals(['c:20', 'a:5', 'a:10', 'b:10-15', 'b:30']),
[range_ for range_ in range_set_with_contigs])
# For a RangeSet instantiated *without* a contig map, the iteration order
# is determined by reference_name, start, end.
range_set_no_contigs = ranges.RangeSet(unsorted)
self.assertEqual(
ranges.parse_literals(['a:5', 'a:10', 'b:10-15', 'b:30', 'c:20']),
[range_ for range_ in range_set_no_contigs])
def _from_literals_list(literals, contig_map=None): """Makes a list of Range objects from literals.""" return ranges.parse_literals(literals, contig_map)
def _from_literals_list(literals, contig_map=None):
"""Makes a list of Range objects from literals."""
return ranges.parse_literals(literals, contig_map)