def __lt__(self, other):
"""
Define comparison operator for variants, to allow sorting.
"""
# TODO: deal with ambiguous representations caused by non-left-aligned
# data
if self.chrom != other.chrom:
return chromosome_comp(self.chrom, other.chrom)
elif self.pos_from != other.pos_from:
return self.pos_from < other.pos_from
elif self.pos_to != other.pos_to:
return self.pos_to < other.pos_to
elif self.ref != other.ref:
return self.ref < other.ref
elif self.alt != other.alt:
return self.alt < other.alt
else:
return False
def __lt__(self, other):
if self.chrom == other.chrom:
return self.interval < other.interval
else:
return chromosome_comp(self.chrom, other.chrom)
def test_should_sort_chrom_2_before_chrom_10(self):
self.assertTrue(chromosome_comp('2', '10'))
self.assertFalse(chromosome_comp('10', '2'))
def test_should_sort_non_standard_chroms_lexicographically(self):
self.assertTrue(chromosome_comp("GL000193.1", "GL000193.2"))
self.assertFalse(chromosome_comp("GL000193.2", "GL000193.1"))
def test_should_sort_non_standard_chroms_after_standard_chroms(self):
self.assertTrue(chromosome_comp("MT", "GL000193.1"))
self.assertFalse(chromosome_comp("GL000193.1", "MT"))
def test_should_sort_Y_before_MT(self):
self.assertTrue(chromosome_comp('Y', 'MT'))
self.assertFalse(chromosome_comp('MT', 'Y'))
def test_should_sort_X_before_Y(self):
self.assertTrue(chromosome_comp('X', 'Y'))
self.assertFalse(chromosome_comp('Y', 'X'))
def test_should_sort_22_before_X(self):
self.assertTrue(chromosome_comp('22', 'X'))
self.assertFalse(chromosome_comp('X', '22'))