def test_site_move(self):
dummy_counter = fn.Intersecter.Counter()
sites = [{'chr': 'X', 'pos': 10, 'strand': '+'}] + self.sites
intersecter = fn.Intersecter(sites, self.regions, dummy_counter)
intersecter.intersect()
results = dummy_counter.get_results()
self.assertEquals(1, len(results))
def test_2matches(self):
dummy_counter = fn.Intersecter.Counter()
sites = self.sites + [{'chr': 'X', 'pos': 1010, 'strand': '+'}]
intersecter = fn.Intersecter(sites, self.regions, dummy_counter)
intersecter.intersect()
results = dummy_counter.get_results()
self.assertEquals(2, len(results))
def test_strand(self):
dummy_counter = fn.Intersecter.Counter()
sites = [{'chr': 'X', 'pos': 1000, 'strand': '-'}]
intersecter = fn.Intersecter(sites, self.regions, dummy_counter)
intersecter.intersect()
results = dummy_counter.get_results()
self.assertEquals(0, len(results))
def test_region_move(self):
dummy_counter = fn.Intersecter.Counter()
regions = [{
'chr': 'X',
'start': 90,
'stop': 100,
'strand': '+',
'trans': 'trans1'
}] + self.regions
intersecter = fn.Intersecter(self.sites, regions, dummy_counter)
intersecter.intersect()
results = dummy_counter.get_results()
self.assertEquals(1, len(results))
msg('getting sequences')
trans_seqs = genome_parser.get_trans_seqs(trans_exons)
msg('getting foldings')
trans_folds = rnafold_handler.trans_plfolds(trans_seqs, wind_size=80)
trans_seqs = None
msg('converting coordinates to numpy')
exons_trans = genes_parser.trans_exon2np(trans_exon=trans_exons)
msg('getting wt clip sites')
dels_wt = del_parser_wt.get_first()
msg('intersecting wt')
counter = fn.Intersecter.FoldsCounter(trans_folds, trans_exons, span=200)
inter = fn.Intersecter(dels_wt, exons_trans, counter, strand=False)
inter.intersect()
results_wt = counter.get_results()
with open(out_wt, 'w') as fout:
for site in results_wt:
fout.write(' '.join([str(x) for x in [site[1]] + site[0]]) + '\n')
msg('getting wt clip sites')
dels_mut = del_parser_mut.get_first()
msg('intersecting wt')
counter.restart()
inter = fn.Intersecter(dels_mut, exons_trans, counter, strand=False)
inter.intersect()
results_wt = counter.get_results()
def test_match(self):
dummy_counter = fn.Intersecter.Counter()
intersecter = fn.Intersecter(self.sites, self.regions, dummy_counter)
intersecter.intersect()
results = dummy_counter.get_results()
self.assertEquals(1, len(results))