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adamewing / tldr

Identify and annotate TE-mediated insertions in long-read sequence data
MIT License
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Bug report for tablemeth_nonref.py #12

Closed sunyumail93 closed 3 years ago

sunyumail93 commented 3 years ago

Hi, it's me again.

I found one bug in the tablemeth_nonref.py script. I ran the program using the command: tablemeth_nonref.py -t Data.table.txt --teont_dir Data_TLDR

And I got the following error: TypeError: stat: path should be string, bytes, os.PathLike or integer, not NoneType

I found this was because the teont_dir parameter was not properly passed to the program: teont_dir = None if args.teont_dir is None: teont_dir = '.'.join(args.table.split('.')[:-2]) ... assert os.path.exists(teont_dir)

I suggest to add: else: teont_dir=args.teont_dir after the if statement, so the program can take the argument when providing the path.

sunyumail93 commented 3 years ago

BTW, this also happens in the plotmeth_nonref.py when providing -d parameter

adamewing commented 3 years ago

Thanks! fixed in e824423.