def test_add_feature(self):
contig = EMBLContig()
contig.add_feature(
sequence_id = 1,
feature_type = 'tRNA',
start = 100,
end = 200,
strand = '+',
feature_attributes = {'some_attribute': 'ABC' }
)
self.assertEqual(len(contig.features), 1)
def test_add_ignored_feature(self, feature_mock):
contig = EMBLContig()
feature_mock.return_value.format.side_effect = lambda: None
contig.add_feature(
sequence_id = 1,
feature_type = 'tRNA',
start = 100,
end = 200,
strand = '+',
feature_attributes = {'some_attribute': 'ABC' }
)
self.assertEquals(contig.features, {})
def visit_feature_node(self, feature_node):
sequence_id = feature_node.get_seqid()
contig = self.contigs.get(sequence_id)
if contig: # contig already exists, just try and update it
contig.add_feature(sequence_id=sequence_id,
feature_type=feature_node.get_type(),
start=feature_node.get_start(),
end=feature_node.get_end(),
strand=feature_node.get_strand(),
feature_attributes=feature_node.attribs,
locus_tag=self.locus_tag,
translation_table=self.translation_table)
else:
contig = EMBLContig()
successfully_added_feature = contig.add_feature(
sequence_id=sequence_id,
feature_type=feature_node.get_type(),
start=feature_node.get_start(),
end=feature_node.get_end(),
strand=feature_node.get_strand(),
feature_attributes=feature_node.attribs,
locus_tag=self.locus_tag,
translation_table=self.translation_table)
if successfully_added_feature:
self.contigs[sequence_id] = contig
else:
pass # discard the contig because we didn't add a feature so it is empty
def visit_feature_node(self, feature_node):
sequence_id = feature_node.get_seqid()
contig = self.contigs.get(sequence_id)
if contig: # contig already exists, just try and update it
contig.add_feature(sequence_id = sequence_id, feature_type = feature_node.get_type(), start = feature_node.get_start(),
end = feature_node.get_end(), strand = feature_node.get_strand(),
feature_attributes = feature_node.attribs,
locus_tag = self.locus_tag, translation_table = self.translation_table)
else:
contig = EMBLContig()
successfully_added_feature = contig.add_feature(sequence_id = sequence_id, feature_type = feature_node.get_type(), start = feature_node.get_start(),
end = feature_node.get_end(), strand = feature_node.get_strand(),
feature_attributes = feature_node.attribs,
locus_tag = self.locus_tag, translation_table = self.translation_table)
if successfully_added_feature:
self.contigs[sequence_id] = contig
else:
pass # discard the contig because we didn't add a feature so it is empty
