Jumitti / TFinder

Python script to quickly extract promoter and terminator regions with the NCBI API. Search for the presence of individual pattern or transcription factor responsive elements with manual sequence (IUPAC) or JASPAR API.
https://tfinder-ipmc.streamlit.app/
MIT License
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[BUG] Wrong Gene ID leads to an error and not a warning #37

Closed Jumitti closed 1 year ago

Jumitti commented 1 year ago

Describe the bug Wrong Gene ID leads to an error and not a warning

To Reproduce Steps to reproduce the behavior:

  1. Add an ID invalid (4847)
  2. Extract promoter or terminator
  3. See error
Traceback (most recent call last):
  File "/home/adminuser/venv/lib/python3.11/site-packages/streamlit/runtime/scriptrunner/script_runner.py", line 552, in _run_script
    exec(code, module.__dict__)
  File "/mount/src/tfinder/TFinder-v1.py", line 108, in <module>
    allapp_page()
  File "/mount/src/tfinder/navigation/allapp.py", line 67, in allapp_page
    aio_page()
  File "/mount/src/tfinder/navigation/aio.py", line 251, in aio_page
    all_slice_forms=True if all_variants else False).find_sequences()
                                                     ^^^^^^^^^^^^^^^^

  File "/mount/src/tfinder/tfinder/__init__.py", line 131, in find_sequences
    gene_name, chraccver, chrstart, chrstop, species_API = NCBIdna.get_gene_info(entrez_id)
                                                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/mount/src/tfinder/tfinder/__init__.py", line 222, in get_gene_info
    return gene_name, _, _, _, _
                      ^
NameError: name '_' is not defined
Jumitti commented 1 year ago

Done