def setUp(self):
test_identifier1 = 3
test_indices1 = [3734, 4034]
test_score1 = 0.9
test_parent_id1 = 2
self.test_exon0 = Exon(identifier=test_identifier1, indices=test_indices1, score=test_score1, parent_id=test_parent_id1)
self.extra_identifiers = [4, 5, 6, 7]
self.extra_scores = [0.9, 0.9, 0.9, 0.9]
self.extra_indices = [[4092, 4332], [4399, 5185], [5249, 6565], [6630, 7436]]
self.test_exon1 = Exon(identifier=test_identifier1, indices=test_indices1, score=test_score1, parent_id=test_parent_id1)
for ind_pair in self.extra_indices:
self.test_exon1.add_indices(ind_pair)
for ident in self.extra_identifiers:
self.test_exon1.add_identifier(ident)
for score in self.extra_scores:
self.test_exon1.add_score(score)
def process_exon_line(self, line):
"""Extracts arguments from a line and adds them to a Exon, or makes a new one."""
kwargs = self.extract_exon_args(line)
if not kwargs:
return
parent_id = kwargs['parent_id']
if parent_id not in self.mrnas:
self.orphans.append(line)
return
parent_mrna = self.mrnas[parent_id]
if parent_mrna.exon:
self.update_exon(line, parent_mrna.exon)
else:
parent_mrna.exon = Exon(**kwargs)