def testSingleLocation(self):
location = Location.from_location_str('join(311,400..854)')
self.assertTrue(location.intersects(Location.from_location((311, ))),
"Location doesn't contain target point")
location = Location.from_location_str('join(14424..14857,1)')
self.assertTrue(location.intersects(Location.from_location((1, ))),
"Location doesn't contain target point")
def testSingleLocationWithTolerance(self):
location = Location.from_location_str(
'join(<10,61..86,162..203,264..318,388..>495)', tolerance=10)
self.assertTrue(location.intersects(Location.from_location((5, ))),
"Location doesn't contain target point")
location = Location.from_location_str('join(<1..129,>657)',
tolerance=10)
self.assertTrue(location.intersects(Location.from_location((660, ))),
"Location doesn't contain target point")
def testParsesMultisegmentLocation(self):
location = Location.from_location_str(
'join(AF178221.1:<1..60,AF178222.1:1..63,AF178223.1:1..42, 1..>90)'
)
self.assertTrue(location.intersects(Location.from_location((80, ))),
"Location doesn't contain target point")
self.assertIn('AF178221.1', location.references(),
'Reference AF178221.1 not parsed')
self.assertIn('AF178222.1', location.references(),
'Reference AF178222.1 not parsed')
self.assertIn('AF178223.1', location.references(),
'Reference AF178223.1 not parsed')
self.assertTrue(
len(location.references()) == 3, 'Wrong number of references')
def testIntersections(self):
location = Location.from_location_str(
"complement(join(<197..1301,2070..>2451))")
self.assertFalse(location.intersects(Location.from_location((100, ))))
self.assertFalse(
location.intersects(
Location.from_location((100, ), complement=True)))
self.assertFalse(location.intersects(Location.from_location((300, ))))
self.assertTrue(
location.intersects(
Location.from_location((300, ), complement=True)))
self.assertFalse(location.intersects(Location.from_location(
(50, 100))))
self.assertFalse(
location.intersects(
Location.from_location((50, 100), complement=True)))
self.assertFalse(
location.intersects(Location.from_location((300, 400))))
self.assertTrue(
location.intersects(
Location.from_location((300, 400), complement=True)))
self.assertFalse(
location.intersects(Location.from_location((1200, 1400))))
self.assertTrue(
location.intersects(
Location.from_location((1200, 1400), complement=True)))
def matches(self, location, complement, tolerance):
l1 = Location.from_location_str(self.location, tolerance)
return l1.intersects(Location.from_location(location, complement))
def testIntersectionDifferentStrands(self):
loc1 = Location.from_location(location_tuple=(1, 2), complement=True)
loc2 = Location.from_location(location_tuple=(1, 2), complement=False)
self.assertEqual(None, loc1.find_intersection(loc2))
def testParseReferenceLocation(self):
location = Location.from_location_str('REFERENCE:1..10')
self.assertTrue(location.intersects(Location.from_location((5, 15))))
def testParseOrderLocation(self):
location = Location.from_location_str('order(1..3,4..6)')
self.assertTrue(location.intersects(Location.from_location((3, 4))),
"Location doesn't contain target point")
def testParsesLocationWithSpaces(self):
location = Location.from_location_str(
'join(620..987, 1010..1170,1194..1443)')
self.assertTrue(location.intersects(Location.from_location((1010, ))),
"Location doesn't contain target point")
def matches(self, location, complement, tolerance):
l1 = Location.from_location_str(self.location, tolerance)
return l1.intersects(Location.from_location(location, complement))
