def test_extract(self):
"""LocationList extract should return correct sequence"""
l = Location(3)
l2_a = Location(5)
l2_b = Location(7)
l2 = Location([l2_a, l2_b], Strand=-1)
l3_a = Location(10)
l3_b = Location(12)
l3 = Location([l3_a, l3_b])
ll = LocationList([l, l2, l3])
s = ll.extract("ACGTGCAGTCAGTAGCAT")
# 123456789012345678
self.assertEqual(s, "G" + "TGC" + "CAG")
# check a case where it wraps around
l5_a = Location(16)
l5_b = Location(4)
l5 = Location([l5_a, l5_b])
ll = LocationList([l5])
s = ll.extract("ACGTGCAGTCAGTAGCAT")
self.assertEqual(s, "CATACGT")
def test_init(self):
"""Location should init with 1 or 2 values, plus params."""
l = Location(37)
self.assertEqual(str(l), "37")
l = Location(37, Ambiguity=">")
self.assertEqual(str(l), ">37")
l = Location(37, Ambiguity="<")
self.assertEqual(str(l), "<37")
l = Location(37, Accession="AB123")
self.assertEqual(str(l), "AB123:37")
l = Location(37, Accession="AB123", Db="Kegg")
self.assertEqual(str(l), "Kegg::AB123:37")
l1 = Location(37)
l2 = Location(42)
l = Location([l1, l2])
self.assertEqual(str(l), "37..42")
l3 = Location([l1, l2], IsBounds=True)
self.assertEqual(str(l3), "(37.42)")
l4 = Location([l1, l2], IsBetween=True)
self.assertEqual(str(l4), "37^42")
l5 = Location([l4, l3])
self.assertEqual(str(l5), "37^42..(37.42)")
l5 = Location([l4, l3], Strand=-1)
self.assertEqual(str(l5), "complement(37^42..(37.42))")