Open joseph-siefert opened 5 months ago
Both of the following code blocks give similar errors:
from pybiomart import Server server = Server(host='http://www.ensembl.org') dataset = (server.marts['ENSEMBL_MART_ENSEMBL'] .datasets['hsapiens_gene_ensembl']) dataset.query(attributes=['ensembl_gene_id', 'external_gene_name'], filters={'chromosome_name': ['1','2']}) Traceback (most recent call last): File /mambaforge/envs/scanpy/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3550 in run_code exec(code_obj, self.user_global_ns, self.user_ns) Cell In[12], line 5 dataset = (server.marts['ENSEMBL_MART_ENSEMBL'] File /mambaforge/envs/scanpy/lib/python3.9/site-packages/pybiomart/server.py:61 in marts self._marts = self._fetch_marts() File /mambaforge/envs/scanpy/lib/python3.9/site-packages/pybiomart/server.py:81 in _fetch_marts xml = xml_from_string(response.content) File /mambaforge/envs/scanpy/lib/python3.9/xml/etree/ElementTree.py:1342 in XML parser.feed(text) File <string> ParseError: mismatched tag: line 62, column 2
from pybiomart import Dataset dataset = Dataset(name='hsapiens_gene_ensembl', host='http://www.ensembl.org') dataset.query(attributes=['ensembl_gene_id', 'external_gene_name'], filters={'chromosome_name': ['1','2']}) Traceback (most recent call last): File /mambaforge/envs/scanpy/lib/python3.9/site-packages/IPython/core/interactiveshell.py:3550 in run_code exec(code_obj, self.user_global_ns, self.user_ns) Cell In[13], line 6 dataset.query(attributes=['ensembl_gene_id', 'external_gene_name'], File /mambaforge/envs/scanpy/lib/python3.9/site-packages/pybiomart/dataset.py:243 in query attr = self.attributes[name] File /mambaforge/envs/scanpy/lib/python3.9/site-packages/pybiomart/dataset.py:99 in attributes self._filters, self._attributes = self._fetch_configuration() File /mambaforge/envs/scanpy/lib/python3.9/site-packages/pybiomart/dataset.py:152 in _fetch_configuration xml = ElementTree.fromstring(response.content) File /mambaforge/envs/scanpy/lib/python3.9/xml/etree/ElementTree.py:1342 in XML parser.feed(text) File <string> ParseError: mismatched tag: line 62, column 2
Package versions:
pybiomart 0.2.0 Python 3.9.18
https://www.ensembl.info/category/07-status/
The blog post says that it has been fixed, but I am still getting the same error that is reported here. Does anyone else still get this error?
Both of the following code blocks give similar errors:
Package versions: