def features(self):
"""list: Get the features from the feature file, metadata file, or in memory"""
if self.feature_file:
log.debug('{}: reading features from feature file {}'.format(self.id, self.feature_path))
with open(self.feature_path) as handle:
feats = list(GFF.parse(handle))
if len(feats) > 1:
log.warning('Too many sequences in GFF')
else:
return feats[0].features
elif self.metadata_file:
log.debug('{}: reading features from metadata file {}'.format(self.id, self.metadata_path))
tmp_sr = SeqIO.read(self.metadata_path, 'uniprot-xml')
return tmp_sr.features
else:
return self._features
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