def test_no_landmark(self):
"""Landmark is missing on this chromosome / stramd."""
xlinks = make_file_from_list([
['chrX', '22', '23', '.', '3', '+'],
])
distances, total_cdna = rnamaps.compute_distances(
self.landmarks, xlinks, 'exon-intron')
self.assertEqual(total_cdna, 3)
self.assertEqual(distances, {})
def test_basic(self):
xlinks = make_file_from_list([
['chr1', '12', '13', '.', '3', '+'],
])
distances, total_cdna = rnamaps.compute_distances(
self.landmarks, xlinks, 'exon-intron')
self.assertEqual(total_cdna, 3)
self.assertEqual(distances, {
'chr1__+__10__G1': {
2: 3
},
})
def test_size_limit(self):
xlinks = make_file_from_list([
['chr1', '22', '23', '.', '3', '+'],
['chr2', '222', '223', '.', '1', '+'],
])
distances, total_cdna = rnamaps.compute_distances(
self.landmarks, xlinks, 'exon-intron')
self.assertEqual(total_cdna, 4)
self.assertEqual(distances, {
'chr1__+__20__G1': {
2: 3
},
})
def test_chroms_not_mixed(self):
xlinks = make_file_from_list([
['chr1', '12', '13', '.', '3', '+'],
['chr2', '12', '13', '.', '1', '+'],
])
distances, total_cdna = rnamaps.compute_distances(
self.landmarks, xlinks, 'exon-intron')
self.assertEqual(total_cdna, 4)
self.assertEqual(distances, {
'chr1__+__10__G1': {
2: 3
},
'chr2__+__10__G3': {
2: 1
},
})