def test_second_start_segmentation(self):
segmentation = {
'G001': {
'gene_segment': [],
'T0001': [
pybedtools.create_interval_from_list(
['1', '.', 'exon', '100', '200', '.', '+', '.',
'gene_id: "G001"', 'transcript_id: "T0001"']),
],
},
'G002': {
'gene_segment': [],
'T0002': [
pybedtools.create_interval_from_list(
['1', '.', 'exon', '50', '100', '.', '-', '.',
'gene_id: "G001"', 'transcript_id: "T0001"']),
],
},
}
second_start, _ = xlsites._second_start(
read=0, poss=(1, 2, 99, 100), strand='+', chrom=1,
segmentation=segmentation, holesize_th=4)
self.assertEqual(second_start, 99)
second_start, _ = xlsites._second_start(
read=0, poss=(99, 100, 199, 200), strand='-', chrom=1,
segmentation=segmentation, holesize_th=4)
self.assertEqual(second_start, 100)
second_start, _ = xlsites._second_start(
read=0, poss=(1, 2, 4, 5), strand='-', chrom=1,
segmentation=segmentation, holesize_th=4)
self.assertEqual(second_start, 2)
def test_second_start_no_seg(self):
# If hole size is lower than holesize_th, strange should be empty:
_, is_strange = xlsites._second_start(
read='the_read', poss=(1, 2, 5, 6), strand='+', chrom=1,
segmentation=None, holesize_th=1)
self.assertTrue(is_strange)
# If hole size is lower than holesize_th, strange should be empty:
_, is_strange = xlsites._second_start(
read='the_read', poss=(1, 2, 5, 6), strand='+', chrom=1,
segmentation=None, holesize_th=2)
self.assertFalse(is_strange)
def test_second_start_no_annotation(self):
# If hole size is lower than holesize_th, strange should be empty:
strange = []
xlsites._second_start(read='the_read',
poss=(1, 2, 5, 6),
strange=strange,
strand='+',
chrom=1,
annotation=None,
holesize_th=1)
self.assertEqual(strange, ['the_read'])
# If hole size is lower than holesize_th, strange should be empty:
strange = []
xlsites._second_start(read='the_read',
poss=(1, 2, 5, 6),
strange=strange,
strand='+',
chrom=1,
annotation=None,
holesize_th=2)
self.assertEqual(strange, [])