def __getitem__(self, key):
if isinstance(key, Feature):
key = key.id
c = self.conn.cursor()
try:
c.execute(constants._SELECT + ' WHERE id = ?', (key,))
except sqlite3.ProgrammingError:
c.execute(
constants._SELECT + ' WHERE id = ?',
(key.decode(self.default_encoding),))
results = c.fetchone()
# TODO: raise error if more than one key is found
if results is None:
raise FeatureNotFoundError(key)
return self._feature_returner(**results)
def get_gene_id_by_name(self, gene_name, select_longest=True):
try:
gene_id_list = self._gene_name_to_id_list[gene_name]
except KeyError:
raise FeatureNotFoundError(gene_name)
if len(gene_id_list) == 1:
gene_id = gene_id_list[0]
else:
if select_longest:
gene_id = self._select_longest_id(gene_id_list)
else:
raise ValueError(
f'gene_name {gene_name} corresponding to {len(gene_id_list)} '
f'{len(gene_id_list)} transcripts: {gene_id_list}. But '
f'select_longest=False.')
return gene_id