New error when using db2db:
babessell1 opened this issue · comments
Have used BioDbNet's db2db with no issue for a long time and I recently updated my docker to find this issue when using the arguments:
input_db = 'Ensembl Gene ID'
output_db = ['Gene Symbol', 'Gene ID', 'Chromosomal Location']
input_values = a list of ENSEMBL ID's
TAXON = 9606
Traceback (most recent call last):
File "/usr/local/lib/python3.8/dist-packages/bioservices/biodbnet.py", line 148, in db2db
df.set_index("InputValue", inplace=True)
File "/usr/local/lib/python3.8/dist-packages/pandas/core/frame.py", line 4727, in set_index
raise KeyError(f"None of {missing} are in the columns")
KeyError: "None of ['InputValue'] are in the columns"
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "rnaseq_preprocess.py", line 280, in
main(sys.argv[1:])
File "rnaseq_preprocess.py", line 273, in main
handle_tissue_batch(tissue_names, mode, technique, form, taxon_id)
File "rnaseq_preprocess.py", line 131, in handle_tissue_batch
create_gene_info_file(tissue_name, count_matrix_file, form, taxon_id, gene_output_dir)
File "rnaseq_preprocess.py", line 94, in create_gene_info_file
gene_info = fetch_gene_info(genes, input_db=form, output_db=output_db, taxon_id=taxon_id)
File "rnaseq_preprocess.py", line 49, in fetch_gene_info
df_test = s.db2db(input_db, output_db, input_values[i:upper_range], taxon_id)
File "/usr/local/lib/python3.8/dist-packages/bioservices/biodbnet.py", line 152, in db2db
self.logging.error(err)
AttributeError: 'BioDBNet' object has no attribute 'logging'
Any help would be greatly appreciated!
Never mind, I had accidentally made a typo when I refactored causing an empty list to be queried. It is still true that there is a problem with the logging feature in bioDBNet if it has a chance to reach that exception.