BacTermFinder must be run from the repository directory and the input cannot be in a different directory

[havranej]

Hello!

I am currently testing BacTermFinder and I have encountered two inconvenient issues which do not output informative errors.

1) When I run BacTermFinder from a directory different from the cloned repo, I get the following error:

python: can't open file '/home/jan/tmp/bactermfinder-test/iLearnPlus/util/FileProcessing.py': [Errno 2] No such file or directory
Traceback (most recent call last):
  File "/home/jan/tmp/bactermfinder-test/BacTermFinder/genome_scan.py", line 225, in <module>
    files = os.listdir('output_sample')

2) When I set my working directory to be in the repo directory, but try to specify input which is located elsewhere (such as ../sequence.fna with the output path being set to out), I get the following error:

Traceback (most recent call last):
  File "/home/jan/tmp/bactermfinder-test/BacTermFinder/genome_scan.py", line 202, in <module>
    df_slide.to_csv(output_file.split(".")[0] + f'_{genome_file}_sliding_windows.csv',
  File "/home/jan/anaconda3/envs/bactermfinder/lib/python3.9/site-packages/pandas/util/_decorators.py", line 211, in wrapper
    return func(*args, **kwargs)
  File "/home/jan/anaconda3/envs/bactermfinder/lib/python3.9/site-packages/pandas/core/generic.py", line 3721, in to_csv
    return DataFrameRenderer(formatter).to_csv(
  File "/home/jan/anaconda3/envs/bactermfinder/lib/python3.9/site-packages/pandas/util/_decorators.py", line 211, in wrapper
    return func(*args, **kwargs)
  File "/home/jan/anaconda3/envs/bactermfinder/lib/python3.9/site-packages/pandas/io/formats/format.py", line 1189, in to_csv
    csv_formatter.save()
  File "/home/jan/anaconda3/envs/bactermfinder/lib/python3.9/site-packages/pandas/io/formats/csvs.py", line 241, in save
    with get_handle(
  File "/home/jan/anaconda3/envs/bactermfinder/lib/python3.9/site-packages/pandas/io/common.py", line 735, in get_handle
    check_parent_directory(str(handle))
  File "/home/jan/anaconda3/envs/bactermfinder/lib/python3.9/site-packages/pandas/io/common.py", line 598, in check_parent_directory
    raise OSError(rf"Cannot save file into a non-existent directory: '{parent}'")
OSError: Cannot save file into a non-existent directory: 'out_..'

Would it be possible to address fix issues, please? They are very much limiting the practical usage of the tool

[AminTaheri23]

Hello Jan,

Sorry for the late reply. I'll look into it asap if your issue still persists.

Thanks Amin