def setUp(self):
self.old_bed = Bed("data/rice_t_sorghum_v1/sorghum_v1.bed")
self.missed_bed = Bed(
"data/rice_t_sorghum_v1/missed_sorghum_v1_from_rice_b.bed")
self.matches = "data/rice_t_sorghum_v1/missed_sorghum_v1_from_rice_b.matches.txt"
self.missed_genes = parse_missed_genes(self.matches)
self.missed_genes_grouped, self.missed_genes_dict = group_genes_in_bed(
self.missed_genes, self.old_bed, self.missed_bed)
def test_group_genes_in_bed(self):
missed_genes_grouped, missed_genes_dict = group_genes_in_bed(
self.missed_genes, self.old_bed, self.missed_bed)
### adding to old bed example
self.assertEqual(missed_genes_dict['Sb01g039400']['locs'],
[(62821196, 62822809), (62822899, 62823011)])
#### example with more then one hit for os03
self.assertEqual(
missed_genes_grouped["Os03g06330"],
[('1', 1035243, 1035376, 'sorghum_v1_1_1035243_1035376'),
('1', 43157679, 43159029, 'sorghum_v1_1_43157679_43159029')])
def setUp(self):
self.old_bed = Bed("data/rice_t_sorghum_v1/sorghum_v1.bed")
self.missed_bed = Bed("data/rice_t_sorghum_v1/missed_sorghum_v1_from_rice_b.bed")
self.matches = "data/rice_t_sorghum_v1/missed_sorghum_v1_from_rice_b.matches.txt"
self.missed_genes = parse_missed_genes(self.matches)
self.missed_genes_grouped, self.missed_genes_dict = group_genes_in_bed(self.missed_genes,self.old_bed,self.missed_bed)
def test_group_genes_in_bed(self):
missed_genes_grouped, missed_genes_dict = group_genes_in_bed(self.missed_genes,self.old_bed,self.missed_bed)
### adding to old bed example
self.assertEqual(missed_genes_dict['Sb01g039400']['locs'], [(62821196, 62822809), (62822899, 62823011)])
#### example with more then one hit for os03
self.assertEqual(missed_genes_grouped["Os03g06330"],[('1', 1035243, 1035376, 'sorghum_v1_1_1035243_1035376'), ('1', 43157679, 43159029, 'sorghum_v1_1_43157679_43159029')])
