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rraadd88 / beditor

A Computational Workflow for Designing Libraries of sgRNAs for CRISPR-Mediated Base Editing, and much more
GNU General Public License v3.0
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input file format #14

Closed neko-ni closed 2 years ago

neko-ni commented 3 years ago

I am confuse when supporting the tsv input file. I try to use the example file for S. cerevisiae . I am not sure what's the form of genome coordinate.So i just use the first two rows of the example.But it can't go well. Is that a bug or something? ########## Namespace(cfg=None, force=False, step=None, test=False) Traceback (most recent call last): File "/public1/users/sunmw/miniconda3/envs/beditor/bin/beditor", line 8, in sys.exit(main()) File "/public1/users/sunmw/miniconda3/envs/beditor/lib/python3.6/site-packages/beditor/pipeline.py", line 465, in main gui(test=args.test) File "/public1/users/sunmw/miniconda3/envs/beditor/lib/python3.6/site-packages/beditor/gui.py", line 552, in gui din=din.rename(columns={c:normalised2cols[normalisestr(c)] for c in din}) File "/public1/users/sunmw/miniconda3/envs/beditor/lib/python3.6/site-packages/beditor/gui.py", line 552, in din=din.rename(columns={c:normalised2cols[normalisestr(c)] for c in din}) KeyError: 'i147494147494' #################### tsv file is like: I:147494-147494- A I:143607-143607+ A Is there something I do wrong? Thanks a lot! @rraadd88

rraadd88 commented 3 years ago

Hi @neko-ni, Could you please try the command-line mode and see if you get the same error? Also, for your trial and specifically for the format of input file, you could try this example file? Please let me know if that works. I will be able to troubleshoot the issue accordingly.