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_sequence_node(self, sequence_node):
sequence_id = sequence_node.get_description()
contig = self.contigs.setdefault(sequence_id, EMBLContig())
contig.add_sequence(sequence_node.get_sequence())
