def test_eq(self):
r1 = Region(self.fai_path, 'chr22:1-10000')
r2 = Region(self.fai_path, 'chr22:1-10000')
self.assertTrue(r1 == r2)
r3 = Region(self.fai_path, 'chr22')
self.assertFalse(r2 == r3)
def test_lt(self):
r1 = Region(self.fai_path, 'chr22:1-10000')
r2 = Region(self.fai_path, 'chrHLA:1:2:3:4:1-10000')
self.assertTrue(r1 < r2)
r3 = Region(self.fai_path, 'chr22')
self.assertTrue(r3 < r1)
r4 = Region(self.fai_path, 'chr22:10000')
self.assertTrue(r3 < r4)
self.assertTrue(r1 < r4)
def test_short_region(self):
regions = {'chr22': '100', 'chrHLA:1:2:3:4': '1000'}
for chrom, start in regions.iteritems():
r = Region(self.fai_path, ':'.join((chrom, str(start))))
self.assertEqual(r.chrom, chrom)
self.assertEqual(r.start, start)
self.assertIsNone(r.end)
def test_chromosome_only(self):
regions = ['chr22', 'chrHLA:1:2:3:4']
for region in regions:
r = Region(self.fai_path, region)
self.assertEqual(r.chrom, region)
self.assertIsNone(r.start)
self.assertIsNone(r.end)
def test_long_region(self):
regions = {'chr22': ('100', '999'), 'chrHLA:1:2:3:4': ('1000', '1100')}
for chrom, positions in regions.iteritems():
r = Region(self.fai_path, ':'.join(
(chrom, '-'.join(map(str, positions)))))
self.assertEqual(r.chrom, chrom)
self.assertEqual(r.start, positions[0])
self.assertEqual(r.end, positions[1])
def chromosome_key(task):
reference_fai = os.path.join(
'/gscmnt/ams1102/info/model_data/2869585698/build106942997',
'all_sequences.fa.fai')
return Region(reference_fai, task.params['in_chrom']).chrom
def chromosome_key(task):
reference_fai = '/gscmnt/gc2802/halllab/ccdg_resources/genomes/human/GRCh38DH/all_sequences.fa.fai'
return Region(reference_fai, task.params['in_chrom']).chrom
def test_sort(self):
r1 = Region(self.fai_path, 'chr22:1-10000')
r2 = Region(self.fai_path, 'chrHLA:1:2:3:4:1-10000')
r3 = Region(self.fai_path, 'chr22:10001-20000')
r4 = Region(self.fai_path, 'chr22:10001-20001')
self.assertEqual([r1, r3, r4, r2], sorted([r4, r3, r2, r1]))
def test_hash(self):
r1 = Region(self.fai_path, 'chr22:1-10000')
r2 = Region(self.fai_path, 'chr22:1-10000')
self.assertEqual(r1.__hash__(), r2.__hash__())
def test_end_lt(self):
self.assertFalse(Region._end_lt('22', '10'))
self.assertTrue(Region._end_lt('22', None))
self.assertFalse(Region._end_lt(None, None))
self.assertFalse(Region._end_lt(None, '1'))
self.assertTrue(Region._end_lt('1', '10'))
def test_invalid_chromosome(self):
with self.assertRaises(RuntimeError):
r = Region(self.fai_path, 'gobbeldygook')